Crystal structures of bacterial guanylate kinases

ABSTRACT

The present invention relates to novel drug targets for pathogenic bacteria. Accordingly, the invention provides purified protein comprising the amino acid sequence set forth in SEQ ID NO: 4. The invention also provides biochemical and biophysical characteristics of the polypeptides of the invention.

RELATED APPLICATION INFORMATION

This application is a continuation-in-part of International ApplicationNo. PCT/CA03/01673, filed Nov. 5, 2003, which claims the benefit ofpriority to the following U.S. Provisional Patent Applications, all ofwhich applications are hereby incorporated by reference in theirentirety. Provisional Application Number Attorney Docket Number FilingDate 60/423,736 IPT-341.60 Nov. 5, 2002 60/432,779 IPT-341.61 Dec. 12,2002

INTRODUCTION

The discovery of novel antimicrobial agents that work by novelmechanisms is a problem researchers in all fields of drug developmentface today. The increasing prevalence of drug-resistant pathogens(bacteria, fungi, parasites, etc.) has led to significantly highermortality rates from infectious diseases and currently presents aserious crisis worldwide. Despite the introduction of second and thirdgeneration antimicrobial drugs, certain pathogens have developedresistance to all currently available drugs.

One of the problems contributing to the development of multiple drugresistant pathogens is the limited number of protein targets forantimicrobial drugs. Many of the antibiotics currently in use arestructurally related or act through common targets or pathways.Accordingly, adaptive mutation of a single gene may render a pathogenicspecies resistant to multiple classes of antimicrobial drugs. Therefore,the rapid discovery of drug targets is urgently needed in order tocombat the constantly evolving threat by such infectious microorganisms.

Recent advances in bacterial and viral genomics research provides anopportunity for rapid progress in the identification of drug targets.The complete genomic sequences for a number of microorganisms areavailable. However, knowledge of the complete genomic sequence is onlythe first step in a long process toward discovery of a viable drugtarget. The genomic sequence must be annotated to identify open readingframes (ORFs), the essentiality of the protein encoded by the ORF mustbe determined and the mechanism of action of the gene product must bedetermined in order to develop a targeted approach to drug discovery.

There are a variety of computer programs available to annotate genomicsequences. Genome annotation involves both identification of genes aswell assignment of function thereto based on sequence comparison tohomologous proteins with known or predicted functions. However, genomeannotation has turned out to be much more of an art than a science.Factors such as splice variants and sequencing errors coupled with theparticular algorithms and databases used to annotate the genome canresult in significantly different annotations for the same genome. Forexample, upon reanalysis of the genome of Mycoplasma pneumoniae usingmore rigorous sequence comparisons coupled with molecular biologicaltechniques, such as gel electrophoresis and mass spectrometry,researchers were able to identify several previously unidentified codingsequences, to dismiss a previous identified coding sequence as a likelypseudogene, and to adjust the length of several previously defined ORFs(Dandkar et al. (2000) Nucl. Acids Res. 28(17): 3278-3288). Furthermore,while overall conservation between amino acid sequences generallyindicates a conservation of structure and function, specific changes atkey residues can lead to significant variation in the biochemical andbiophysical properties of a protein. In a comparison of three differentfunctional annotations of the Mycoplasma genitalium genome, it wasdiscovered that some genes were assigned three different functions andit was estimated that the overall error rate in the annotations was atleast 8% (Brenner (1999) Trends Genet 15(4): 132-3). Accordingly,molecular biological techniques are required to ensure proper genomeannotation and identify valid drug targets.

However, confirmation of genome annotation using molecular biologicaltechniques is not an easy proposition due to the unpredictability inexpression and purification of polypeptide sequences. Further, in orderto carry out structural studies to validate proteins as potential drugtargets, it is generally necessary to modify the native proteins inorder to facilitate these analyses, e.g., by labeling the protein (e.g.,with a heavy atom, isotopic label, polypeptide tag, etc.) or by creatingfragments of the polypeptide corresponding to functional domains of amulti-domain protein. Moreover, it is well-known that even small changesin the amino acid sequence of a protein may lead to dramatic affects onprotein solubility (Eberstadt et al. (1998) Nature 392: 941-945).Accordingly, genome-wide validation of protein targets will requireconsiderable effort even in light of the sequence of the entire genomeof an organism and/or purification conditions for homologs of aparticular target.

We have developed reliable, high throughput methods to address some ofthe shortcomings identified above. In part, using these methods, we havenow identified, expressed, and purified a novel antimicrobial targetfrom Enterococcus faecalis, or E. faecalis. Various biophysical,bioinformatic and biochemical studies have been used to characterize thestructure and function of the polypeptides of the invention. TABLE OFCONTENTS RELATED APPLICATION INFORMATION 1 INTRODUCTION 1 TABLE OFCONTENTS 3 SUMMARY OF THE INVENTION 4 BRIEF DESCRIPTION OF THE FIGURES 6DETAILED DESCRIPTION OF THE INVENTION 9  1. Definitions 9  2.Polypeptides of the Invention 26  3. Nucleic Acids of the Invention 38 4. Homology Searching of Nucleotide and Polypeptide 48 Sequences  5.Analysis of Protein Properties 48 (a) Analysis of Proteins by MassSpectrometry 48 (b) Analysis of Proteins by Nuclear Magnetic 51Resonance (NMR) (c) Analysis of Proteins by X-ray 57 Crystallography  6.Interacting Proteins 74  7. Antibodies 87  8. Diagnostic Assays 90  9.Drug Discovery 93 (b) In Vitro Assays 103 (c) In Vivo Assays 105 10.Vaccines 107 11. Array Analysis 109 12. Pharmaceutical Compositions 11213. Antimicrobial Agents 112 14. Other Embodiments 113 EXEMPLIFICATION128 EXAMPLE 1 Isolation and Cloning of Nucleic Acid 128 EXAMPLE 2 TestProtein Expression and Solubility 130 EXAMPLE 3 Native ProteinExpression 131 EXAMPLE 4 Expression of Selmet Labeled Polypeptides 132EXAMPLE 5 Expression of ¹⁵N Labeled Polypeptides 134 EXAMPLE 6 MethodOne for Purifying Polypeptides of 135 the Invention EXAMPLE 7 Method Twofor Purifying Polypeptides of 136 the Invention EXAMPLE 8 Method Threefor Purifying Polypeptides of 137 the Invention EXAMPLE 9 MassSpectrometry Analysis via Fingerprint 138 Mapping EXAMPLE 10 MassSpectrometry Analysis via High Mass 140 EXAMPLE 11 Method One forIsolating and Identifying 141 Interacting Proteins EXAMPLE 12 Method Twofor Isolating and Identifying 144 Interacting Proteins EXAMPLE 13 Samplefor Mass Spectrometry of 145 Interacting Proteins EXAMPLE 14 MassSpectrometric Analysis of Interacting 146 Proteins EXAMPLE 15 NMRAnalysis 148 EXAMPLE 16 X-ray Crystallography 149 EXAMPLE 17 Annotations157 EXAMPLE 18 Essential Gene Analysis 158 EXAMPLE 19 PDB Analysis 159EXAMPLE 20 Virtual Genome Analysis 159 EXAMPLE 21 Epitopic Regions 160EQUIVALENTS 160 164

SUMMARY OF THE INVENTION

As part of an effort at genome-wide structural and functionalcharacterization of microbial targets, the present invention providespolypeptides from E. faecalis. In various aspects, the inventionprovides the nucleic acid and amino acid sequences of the polypeptidesof the invention. The invention also provides purified, soluble forms ofthe polypeptides of the invention suitable for structural and functionalcharacterization using a variety of techniques, including, for example,affinity chromatography, mass spectrometry, NMR and x-raycrystallography. The invention further provides modified versions of thepolypeptides of the invention to facilitate characterization, includingpolypeptides labeled with isotopic or heavy atoms and fusion proteins.

A polypeptide of the invention has been crystallized and its structuresolved as described in detail below, thereby providing information aboutthe structure of the polypeptide, and druggable regions, domains and thelike contained therein, all of which may be used in rational-based drugdesign efforts.

In general, the biological activity of a polypeptide of the invention isexpected to be characterized as having a biochemical activitysubstantially similar to that of guanylate kinase, having the genedesignation of gmk, as described in more detail below. This assignmenthas been confirmed by solving the X-ray structure of a polypeptide ofthe invention.

All of the information learned and described herein about thepolypeptides of the invention may be used to design modulators of one ormore of their biological activities. In particular, information criticalto the design of therapeutic and diagnostic molecules, including, forexample, the protein domain, druggable regions, structural information,and the like for the polypeptides of the invention is now available orattainable as a result of the ability to prepare, purify andcharacterize them, and domains, fragments, variants and derivativesthereof.

In other aspects of the invention, structural and functional informationabout the polypeptides of the invention has and will be obtained. Suchinformation, for example, may be incorporated into databases containinginformation on the polypeptides of the invention, as well as otherpolypeptide targets from other microbial species. Such databases willprovide investigators with a powerful tool to analyze the polypeptidesof the invention and aid in the rapid discovery and design oftherapeutic and diagnostic molecules.

In another aspect, modulators, inhibitors, agonists or antagonistsagainst the polypeptides of the invention, or biological complexescontaining them, or orthologues thereto, may be used to treat anydisease or other treatable condition of a patient (including humans andanimals), and particularly a disease caused by E. faecalis, such as, forexample, one of the following: urinary tract infection, surgical woundinfection, bacteremia, intra abdominal infection, pelvic infection,central nervous system infection, osteomyelitis, pulmonary infection,and endocarditis.

The present invention further allows relationships between polypeptidesfrom the same and multiple species to be compared by isolating andstudying the various polypeptides of the invention and other proteins.By such comparison studies, which may involve multi-variable analysis asappropriate, it is possible to identify drugs that will affect multiplespecies or drugs that will affect one or a few species. In such amanner, so-called “wide spectrum” and narrow spectrum” anti-infectivesmay be identified. Alternatively, drugs that are selective for one ormore bacterial or other non-mammalian species, and not for one or moremammalian species (especially human), may be identified (andvice-versa).

In other embodiments, the invention contemplates kits including thesubject nucleic acids, polypeptides, crystallized polypeptides,antibodies, and other subject materials, and optionally instructions fortheir use. Uses for such kits include, for example, diagnostic andtherapeutic applications.

The embodiments and practices of the present invention, otherembodiments, and their features and characteristics, will be apparentfrom the description, figures and claims that follow, with all of theclaims hereby being incorporated by this reference into this Summary.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the nucleic acid coding sequence for an exemplarypolypeptide of the invention as predicted from the genomic sequence ofE. faecalis (SEQ ID NO: 1). This predicted nucleic acid coding sequencewas cloned and sequenced to produce the polynucleotide sequence shown inFIG. 2 (SEQ ID NO: 3).

FIG. 2 shows the amino acid sequence for an exemplary polypeptide of theinvention as predicted from the nucleotide sequence shown in FIG. 1 (SEQID NO: 2).

FIG. 3 shows the experimentally determined nucleic acid coding sequencefor an exemplary polypeptide of the invention (SEQ ID NO: 3).

FIG. 4 shows the amino acid sequence for the exemplary polypeptide ofthe invention as predicted from the nucleotide sequence shown in FIG. 3(SEQ ID NO: 4).

FIG. 5 shows the primer sequences used to amplify the nucleic acid ofSEQ ID NO: 3. The primers are SEQ ID NO: 5 and SEQ ID NO: 6.

FIG. 6 contains Table 1, which provides among other things a variety ofdata and other information on the polypeptides of the invention.

FIG. 7 contains Table 2, which provides the results of severalbioinformatic analyses relating to SEQ ID NO: 2.

FIG. 8 depicts a ¹H, ¹⁵N Heteronuclear Single Quantum Coherence (HSQC)spectrum. The X-axis shows a proton chemical shift, while the Y-axisshows the ¹⁵N chemical shift of the purified ¹⁵N labeled polypeptide.

FIG. 9 depicts the results of tryptic peptide mass spectrum peaksearching as described in EXAMPLE 9.

FIG. 10 depicts a MALDI-TOF mass spectrum of an intact polypeptide ofthe invention as described in EXAMPLE 10.

FIG. 11 contains Table 3, which shows information related to the x-raystructure for a polypeptide of the invention as described more fully inEXAMPLE 16.

FIG. 12 lists the atomic structure coordinates for a polypeptide of theinvention derived from x-ray diffraction from a crystal of suchpolypeptide, as described in more detail in EXAMPLE 16. There aremultiple pages to FIG. 12. The information in such Figure is presentedin the following tabular format, with a generic entry provided as anexample: Record Header No. Atom Type Residue Residue Number X Y Z OCC BATOM 1 1 CB HIS 1 4.497 15.607 34.172 1 70.54In the table, “Record Header” describes the row type, such as “ATOM”.“No.” refers to the row number. The first “Atom Type” column refers tothe atom whose coordinates are measured, with the first letter in thecolumn identifying the atom by its elemental symbol and the subsequentletter defining the location of the atom in the amino acid residue orother molecule. “Residue” and “residue number” identifies the residue ofthe subject polypeptide. “X, Y, Z” crystallographically define theatomic position of the atom measured. “Occ” is an occupancy factor thatrefers to the fraction of the molecules in which each atom occupies theposition specified by the coordinates. A value of “1” indicates thateach atom has the same conformation, i.e., the same position, in allmolecules of the crystal. “B” is a thermal factor that is related to theroot mean square deviation in the position of the atom around the givenatomic coordinate.

FIG. 13 depicts a clustal V-based sequence alignment of the guanylatekinase protein sequences from six pathogens. The dark shading indicatesconserved amino acids across species, with gray areas less conserved.FIG. 13A depicts a sequence alignment of the E. faecalis guanylatekinase with sequences from six pathogens. The dark shading indicatesconserved amino acids across species, with gray areas less conserved.FIG. 13B a sequence alignment of the E. faecalis guanylate kinase withthe mouse and yeast guanylate kinase sequences

FIG. 14 depicts various representations of the structure of E. faecalisguanylate kinase. FIG. 14A depicts a wireframe structure of E. faecalisguanylate kinase, wherein the residues from the C-terminal tag are shownat the bottom of the structure. These residues have been left out in thesubsequent FIGURES for clarity. Carbon atoms are colored gray, nitrogenatoms colored blue and oxygen atoms colored red. Sulfate atoms aredepicted in orange and red. FIG. 14B depicts a solvent accessiblesurface of the structure in the same orientation as the structure inFIG. 14A. FIG. 14C depicts a ribbon representation of the structure. Thedifferent regions of the structure are color-coded, wherein the COREregion is colored cyan; the NMP-binding region colored red and the LIDregion colored green.

FIG. 15 depicts various representations of the potential binding sitesof ADP and GMP on E. faecalis guanylate kinase. Potential binding siteswere defined using MOE (molecular operating environment, ChemicalComputing Group, 2002). FIG. 15A depicts a ribbon representation of theADP binding site with the binding site residues indicated. Carbon atomsare colored light gray, while oxygen, nitrogen and sulfur atoms arecolored a darker shade of gray. FIG. 15B depicts a ribbon representationof the protein in a different orientation showing the binding site forADP. FIG. 15C depicts the residues surrounding the binding pocket ofGMP. FIG. 15D depicts the protein in a different orientation showing thebinding site for ADP. FIG. 15E depicts the calculated volume of thebinding pocket for GMP, represented by dotted spheres. The red dotsindicate hydrophilic interactions, while the gray dots indicatehydrophobic interactions. FIG. 15F depicts a representation of thecalculated shape of the binding pocket for the yeast guanylate kinasestructure (PDB ID: 1GKY). Note the size and shape of the binding pocketchanges when the protein changes conformation when ligand binds. Thevolume of the pocket was defined using “dummy atoms” that are found insite searches in MOE.

FIG. 16 depicts a comparison of the CORE regions from the yeastguanylate kinase and the E. faecalis guanylate kinase structures. Theyeast structure is depicted as a green ribbon and the E. faecalisstructure as a gray ribbon.

FIG. 17 depicts various representations of sequence conservation mappingonto the structure of the E. faecalis guanylate kinase. The conservationwas calculated using Consurf (Armon, Graur et al. 2001). In theserepresentations, the degree of variation in sequence seen between thesequences of S. aureus, S. pneumonia, H. influenzae, P. aeruginosa andE. coli are mapped onto the E. faecalis structure. FIG. 17A depicts thesequence conservation mapped onto a ribbon diagram of the E. faecalisstructure. Red represents residues that are invariant between sequences,pink represents residues that are more strongly conserved than a typicalresidue, with the degree of redness correlating with the degree ofconservation; white represents residues displaying an average degree ofsequence conservation for this protein, and blue represents residuesthat are more variable than average. In general, residues lining thebinding pocket are well conserved, with the maximally variant residues(in white) showing a tendency to substitute residues that arenonetheless conserved in type and approximate volume (such as Phe andIle substitutions for Tyr). FIG. 17B depicts the sequence conservationmapped to a surface diagram. FIG. 17C depicts the ADP binding siteresidues, while FIG. 17D depicts the GDP binding site residues.

DETAILED DESCRIPTION OF THE INVENTION

1. Definitions

For convenience, certain terms employed in the specification, examples,and appended claims are collected here. Unless defined otherwise, alltechnical and scientific terms used herein have the same meaning ascommonly understood by one of ordinary skill in the art to which thisinvention belongs.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e., to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

The term “amino acid” is intended to embrace all molecules, whethernatural or synthetic, which include both an amino functionality and anacid functionality and capable of being included in a polymer ofnaturally-occurring amino acids. Exemplary amino acids includenaturally-occurring amino acids; analogs, derivatives and congenersthereof; amino acid analogs having variant side chains; and allstereoisomers of any of any of the foregoing.

The term “binding” refers to an association, which may be a stableassociation, between two molecules, e.g., between a polypeptide of theinvention and a binding partner, due to, for example, electrostatic,hydrophobic, ionic and/or hydrogen-bond interactions under physiologicalconditions.

A “comparison window,” as used herein, refers to a conceptual segment ofat least 20 contiguous amino acid positions wherein a protein sequencemay be compared to a reference sequence of at least 20 contiguous aminoacids and wherein the portion of the protein sequence in the comparisonwindow may comprise additions or deletions (i.e., gaps) of 20 percent orless as compared to the reference sequence (which does not compriseadditions or deletions) for optimal alignment of the two sequences.Optimal alignment of sequences for aligning a comparison window may beconducted by the local homology algorithm of Smith and Waterman (1981)Adv. Appl. Math. 2: 482, by the homology alignment algorithm ofNeedleman and Wunsch (1970) J. Mol. Biol. 48: 443, by the search forsimilarity method of Pearson and Lipman (1988) Proc. Natl. Acad. Sci.(U.S.A.) 85: 2444, by computerized implementations of these algorithms(GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics SoftwarePackage Release 7.0, Genetics Computer Group, 575 Science Dr., Madison,Wis.), or by inspection, and the best alignment (i.e., resulting in thehighest percentage of homology over the comparison window) generated bythe various methods may be identified.

The term “complex” refers to an association between at least twomoieties (e.g. chemical or biochemical) that have an affinity for oneanother. Examples of complexes include associations betweenantigen/antibodies, lectin/avidin, target polynucleotide/probeoligonucleotide, antibody/anti-antibody, receptor/ligand, enzyme/ligand,polypeptide/polypeptide, polypeptide/polynucleotide,polypeptide/co-factor, polypeptide/substrate, polypeptide/inhibitor,polypeptide/small molecule, and the like. “Member of a complex” refersto one moiety of the complex, such as an antigen or ligand. “Proteincomplex” or “polypeptide complex” refers to a complex comprising atleast one polypeptide.

The term “conserved residue” refers to an amino acid that is a member ofa group of amino acids having certain common properties. The term“conservative amino acid substitution” refers to the substitution(conceptually or otherwise) of an amino acid from one such group with adifferent amino acid from the same group. A functional way to definecommon properties between individual amino acids is to analyze thenormalized frequencies of amino acid changes between correspondingproteins of homologous organisms (Schulz, G. E. and R. H. Schirmer.,Principles of Protein Structure, Springer-Verlag). According to suchanalyses, groups of amino acids may be defined where amino acids withina group exchange preferentially with each other, and therefore resembleeach other most in their impact on the overall protein structure(Schulz, G. E. and R. H. Schirmer, Principles of Protein Structure,Springer-Verlag). One example of a set of amino acid groups defined inthis manner include: (i) a charged group, consisting of Glu and Asp,Lys, Arg and His, (ii) a positively-charged group, consisting of Lys,Arg and His, (iii) a negatively-charged group, consisting of Glu andAsp, (iv) an aromatic group, consisting of Phe, Tyr and Trp, (v) anitrogen ring group, consisting of His and Trp, (vi) a large aliphaticnonpolar group, consisting of Val, Leu and Ile, (vii) a slightly-polargroup, consisting of Met and Cys, (viii) a small-residue group,consisting of Ser, Thr, Asp, Asn, Gly, Ala, Glu, Gln and Pro, (ix) analiphatic group consisting of Val, Leu, Ile, Met and Cys, and (x) asmall hydroxyl group consisting of Ser and Thr.

The term “domain”, when used in connection with a polypeptide, refers toa specific region within such polypeptide that comprises a particularstructure or mediates a particular function. In the typical case, adomain of a polypeptide of the invention is a fragment of thepolypeptide. In certain instances, a domain is a structurally stabledomain, as evidenced, for example, by mass spectroscopy, or by the factthat a modulator may bind to a druggable region of the domain.

The term “druggable region”, when used in reference to a polypeptide,nucleic acid, complex and the like, refers to a region of the moleculewhich is a target or is a likely target for binding a modulator. For apolypeptide, a druggable region generally refers to a region whereinseveral amino acids of a polypeptide would be capable of interactingwith a modulator or other molecule. For a polypeptide or complexthereof, exemplary druggable regions including binding pockets andsites, enzymatic active sites, interfaces between domains of apolypeptide or complex, surface grooves or contours or surfaces of apolypeptide or complex which are capable of participating ininteractions with another molecule. In certain instances, theinteracting molecule is another polypeptide, which may benaturally-occurring. In other instances, the druggable region is on thesurface of the molecule.

Druggable regions may be described and characterized in a number ofways. For example, a druggable region may be characterized by some orall of the amino acids that make up the region, or the backbone atomsthereof, or the side chain atoms thereof (optionally with or without theCα atoms). Alternatively, in certain instances, the volume of adruggable region corresponds to that of a carbon based molecule of atleast about 200 amu and often up to about 800 amu. In other instances,it will be appreciated that the volume of such region may correspond toa molecule of at least about 600 amu and often up to about 1600 amu ormore.

Alternatively, a druggable region may be characterized by comparison toother regions on the same or other molecules. For example, the term“affinity region” refers to a druggable region on a molecule (such as apolypeptide of the invention) that is present in several othermolecules, in so much as the structures of the same affinity regions aresufficiently the same so that they are expected to bind the same orrelated structural analogs. An example of an affinity region is anATP-binding site of a protein kinase that is found in several proteinkinases (whether or not of the same origin). The term “selectivityregion” refers to a druggable region of a molecule that may not be foundon other molecules, in so much as the structures of differentselectivity regions are sufficiently different so that they are notexpected to bind the same or related structural analogs. An exemplaryselectivity region is a catalytic domain of a protein kinase thatexhibits specificity for one substrate. In certain instances, a singlemodulator may bind to the same affinity region across a number ofproteins that have a substantially similar biological function, whereasthe same modulator may bind to only one selectivity region of one ofthose proteins.

Continuing with examples of different druggable regions, the term“undesired region” refers to a druggable region of a molecule that uponinteracting with another molecule results in an undesirable affect. Forexample, a binding site that oxidizes the interacting molecule (such asP-450 activity) and thereby results in increased toxicity for theoxidized molecule may be deemed a “undesired region”. Other examples ofpotential undesired regions includes regions that upon interaction witha drug decrease the membrane permeability of the drug, increase theexcretion of the drug, or increase the blood brain transport of thedrug. It may be the case that, in certain circumstances, an undesiredregion will no longer be deemed an undesired region because the affectof the region will be favorable, e.g., a drug intended to treat a braincondition would benefit from interacting with a region that resulted inincreased blood brain transport, whereas the same region could be deemedundesirable for drugs that were not intended to be delivered to thebrain.

When used in reference to a druggable region, the “selectivity” or“specificity’ of a molecule such as a modulator to a druggable regionmay be used to describe the binding between the molecule and a druggableregion. For example, the selectivity of a modulator with respect to adruggable region may be expressed by comparison to another modulator,using the respective values of K_(d) (i.e., the dissociation constantsfor each modulator-druggable region complex) or, in cases where abiological effect is observed below the K_(d), the ratio of therespective EC₅₀'s (i.e., the concentrations that produce 50% of themaximum response for the modulator interacting with each druggableregion).

A “fusion protein” or “fusion polypeptide” refers to a chimeric proteinas that term is known in the art and may be constructed using methodsknown in the art. In many examples of fusion proteins, there are twodifferent polypeptide sequences, and in certain cases, there may bemore. The sequences may be linked in frame. A fusion protein may includea domain which is found (albeit in a different protein) in an organismwhich also expresses the first protein, or it may be an “interspecies”,“intergenic”, etc. fusion expressed by different kinds of organisms. Invarious embodiments, the fusion polypeptide may comprise one or moreamino acid sequences linked to a first polypeptide. In the case wheremore than one amino acid sequence is fused to a first polypeptide, thefusion sequences may be multiple copies of the same sequence, oralternatively, may be different amino acid sequences. The fusionpolypeptides may be fused to the N-terminus, the C-terminus, or the N-and C-terminus of the first polypeptide. Exemplary fusion proteinsinclude polypeptides comprising a glutathione S-transferase tag(GST-tag), histidine tag (His-tag), an immunoglobulin domain or animmunoglobulin binding domain.

The term “gene” refers to a nucleic acid comprising an open readingframe encoding a polypeptide having exon sequences and optionally intronsequences. The term “intron” refers to a DNA sequence present in a givengene which is not translated into protein and is generally found betweenexons.

The term “having substantially similar biological activity”, when usedin reference to two polypeptides, refers to a biological activity of afirst polypeptide which is substantially similar to at least one of thebiological activities of a second polypeptide. A substantially similarbiological activity means that the polypeptides carry out a similarfunction, e.g., a similar enzymatic reaction or a similar physiologicalprocess, etc. For example, two homologous proteins may have asubstantially similar biological activity if they are involved in asimilar enzymatic reaction, e.g., they are both kinases which catalyzephosphorylation of a substrate polypeptide, however, they mayphosphorylate different regions on the same protein substrate ordifferent substrate proteins altogether. Alternatively, two homologousproteins may also have a substantially similar biological activity ifthey are both involved in a similar physiological process, e.g.,transcription. For example, two proteins may be transcription factors,however, they may bind to different DNA sequences or bind to differentpolypeptide interactors. Substantially similar biological activities mayalso be associated with proteins carrying out a similar structural role,for example, two membrane proteins.

The term “isolated polypeptide” refers to a polypeptide, in certainembodiments prepared from recombinant DNA or RNA, or of syntheticorigin, or some combination thereof, which (1) is not associated withproteins that it is normally found with in nature, (2) is isolated fromthe cell in which it normally occurs, (3) is isolated free of otherproteins from the same cellular source, e.g. free of other E. faecalisproteins, (4) is expressed by a cell from a different species, or (5)does not occur in nature.

The term “isolated nucleic acid” refers to a polynucleotide of genomic,cDNA, or synthetic origin or some combination there of, which (1) is notassociated with the cell in which the “isolated nucleic acid” is foundin nature, or (2) is operably linked to a polynucleotide to which it isnot linked in nature.

The terms “label” or “labeled” refer to incorporation or attachment,optionally covalently or non-covalently, of a detectable marker into amolecule, such as a polypeptide. Various methods of labelingpolypeptides are known in the art and may be used. Examples of labelsfor polypeptides include, but are not limited to, the following:radioisotopes, fluorescent labels, heavy atoms, enzymatic labels orreporter genes, chemiluminescent groups, biotinyl groups, predeterminedpolypeptide epitopes recognized by a secondary reporter (e.g., leucinezipper pair sequences, binding sites for secondary antibodies, metalbinding domains, epitope tags). Examples and use of such labels aredescribed in more detail below. In some embodiments, labels are attachedby spacer arms of various lengths to reduce potential steric hindrance.

The term “mammal” is known in the art, and exemplary mammals includehumans, primates, bovines, porcines, canines, felines, and rodents(e.g., mice and rats).

The term “modulation”, when used in reference to a functional propertyor biological activity or process (e.g., enzyme activity or receptorbinding), refers to the capacity to either up regulate (e.g., activateor stimulate), down regulate (e.g., inhibit or suppress) or otherwisechange a quality of such property, activity or process. In certaininstances, such regulation may be contingent on the occurrence of aspecific event, such as activation of a signal transduction pathway,and/or may be manifest only in particular cell types.

The term “modulator” refers to a polypeptide, nucleic acid,macromolecule, complex, molecule, small molecule, compound, species orthe like (naturally-occurring or non-naturally-occurring), or an extractmade from biological materials such as bacteria, plants, fungi, oranimal cells or tissues, that may be capable of causing modulation.Modulators may be evaluated for potential activity as inhibitors oractivators (directly or indirectly) of a functional property, biologicalactivity or process, or combination of them, (e.g., agonist, partialantagonist, partial agonist, inverse agonist, antagonist, anti-microbialagents, inhibitors of microbial infection or proliferation, and thelike) by inclusion in assays. In such assays, many modulators may bescreened at one time. The activity of a modulator may be known, unknownor partially known.

The term “motif” refers to an amino acid sequence that is commonly foundin a protein of a particular structure or function. Typically, aconsensus sequence is defined to represent a particular motif. Theconsensus sequence need not be strictly defined and may containpositions of variability, degeneracy, variability of length, etc. Theconsensus sequence may be used to search a database to identify otherproteins that may have a similar structure or function due to thepresence of the motif in its amino acid sequence. For example, on-linedatabases may be searched with a consensus sequence in order to identifyother proteins containing a particular motif. Various search algorithmsand/or programs may be used, including FASTA, BLAST or ENTREZ. FASTA andBLAST are available as a part of the GCG sequence analysis package(University of Wisconsin, Madison, Wis.). ENTREZ is available throughthe National Center for Biotechnology Information, National Library ofMedicine, National Institutes of Health, Bethesda, Md.

The term “naturally-occurring”, as applied to an object, refers to thefact that an object may be found in nature. For example, a polypeptideor polynucleotide sequence that is present in an organism (includingbacteria) that may be isolated from a source in nature and which has notbeen intentionally modified by man in the laboratory isnaturally-occurring.

The term “nucleic acid” refers to a polymeric form of nucleotides,either ribonucleotides or deoxynucleotides or a modified form of eithertype of nucleotide. The terms should also be understood to include, asequivalents, analogs of either RNA or DNA made from nucleotide analogs,and, as applicable to the embodiment being described, single-stranded(such as sense or antisense) and double-stranded polynucleotides.

The term “nucleic acid of the invention” refers to a nucleic acidencoding a polypeptide of the invention, e.g., a nucleic acid comprisinga sequence consisting of, or consisting essentially of, thepolynucleotide sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 3. Anucleic acid of the invention may comprise all, or a portion of: thenucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 3; a nucleotidesequence at least 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98% or 99%identical to SEQ ID NO: 1 or SEQ ID NO: 3; a nucleotide sequence thathybridizes under stringent conditions to SEQ ID NO: 1 or SEQ ID NO: 3;nucleotide sequences encoding polypeptides that are functionallyequivalent to polypeptides of the invention; nucleotide sequencesencoding polypeptides at least about 60%, 70%, 80%, 85%, 90%, 95%, 98%,99% homologous or identical with an amino acid sequence of SEQ ID NO: 2or SEQ ID NO: 4; nucleotide sequences encoding polypeptides having anactivity of a polypeptide of the invention and having at least about60%, 70%, 80%, 85%, 90%, 95%, 98%, 99% or more homology or identity withSEQ ID NO: 2 or SEQ ID NO: 4; nucleotide sequences that differ by 1 toabout 2, 3, 5, 7, 10, 15, 20, 30, 50, 75 or more nucleotidesubstitutions, additions or deletions, such as allelic variants, of SEQID NO: 1 and SEQ ID NO: 3; nucleic acids derived from and evolutionarilyrelated to SEQ ID NO: 1 or SEQ ID NO: 3; and complements of, andnucleotide sequences resulting from the degeneracy of the genetic code,for all of the foregoing and other nucleic acids of the invention.Nucleic acids of the invention also include homologs, e.g., orthologsand paralogs, of SEQ ID NO: 1 or SEQ ID NO: 3 and also variants of SEQID NO: 1 or SEQ ID NO: 3 which have been codon optimized for expressionin a particular organism (e.g., host cell).

The term “operably linked”, when describing the relationship between twonucleic acid regions, refers to a juxtaposition wherein the regions arein a relationship permitting them to function in their intended manner.For example, a control sequence “operably linked” to a coding sequenceis ligated in such a way that expression of the coding sequence isachieved under conditions compatible with the control sequences, such aswhen the appropriate molecules (e.g., inducers and polymerases) arebound to the control or regulatory sequence(s).

The term “phenotype” refers to the entire physical, biochemical, andphysiological makeup of a cell, e.g., having any one trait or any groupof traits.

The term “polypeptide”, and the terms “protein” and “peptide” which areused interchangeably herein, refers to a polymer of amino acids.Exemplary polypeptides include gene products, naturally-occurringproteins, homologs, orthologs, paralogs, fragments, and otherequivalents, variants and analogs of the foregoing.

The terms “polypeptide fragment” or “fragment”, when used in referenceto a reference polypeptide, refers to a polypeptide in which amino acidresidues are deleted as compared to the reference polypeptide itself,but where the remaining amino acid sequence is usually identical to thecorresponding positions in the reference polypeptide. Such deletions mayoccur at the amino-terminus or carboxy-terminus of the referencepolypeptide, or alternatively both. Fragments typically are at least 5,6, 8 or 10 amino acids long, at least 14 amino acids long, at least 20,30, 40 or 50 amino acids long, at least 75 amino acids long, or at least100, 150, 200, 300, 500 or more amino acids long. A fragment can retainone or more of the biological activities of the reference polypeptide.In certain embodiments, a fragment may comprise a druggable region, andoptionally additional amino acids on one or both sides of the druggableregion, which additional amino acids may number from 5, 10, 15, 20, 30,40, 50, or up to 100 or more residues. Further, fragments can include asub-fragment of a specific region, which sub-fragment retains a functionof the region from which it is derived. In another embodiment, afragment may have immunogenic properties.

The term “polypeptide of the invention” refers to a polypeptidecomprising the amino acid sequence set forth in SEQ ID NO: 2 or SEQ IDNO: 4, or an equivalent or fragment thereof, e.g., a polypeptidecomprising a sequence consisting of, or consisting essentially of, theamino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4.Polypeptides of the invention include polypeptides comprising all or aportion of the amino acid sequence set forth in SEQ ID NO: 2 or SEQ IDNO: 4; the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4with 1 to about 2, 3, 5, 7, 10, 15, 20, 30, 50, 75 or more conservativeamino acid substitutions; an amino acid sequence that is at least 60%,70%, 80%, 90%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 2 orSEQ ID NO: 4; and functional fragments thereof. Polypeptides of theinvention also include homologs, e.g., orthologs and paralogs, of SEQ IDNO: 2 or SEQ ID NO: 4.

The term “purified” refers to an object species that is the predominantspecies present (i.e., on a molar basis it is more abundant than anyother individual species in the composition). A “purified fraction” is acomposition wherein the object species comprises at least about 50percent (on a molar basis) of all species present. In making thedetermination of the purity of a species in solution or dispersion, thesolvent or matrix in which the species is dissolved or dispersed isusually not included in such determination; instead, only the species(including the one of interest) dissolved or dispersed are taken intoaccount. Generally, a purified composition will have one species thatcomprises more than about 80 percent of all species present in thecomposition, more than about 85%, 90%, 95%, 99% or more of all speciespresent. The object species may be purified to essential homogeneity(contaminant species cannot be detected in the composition byconventional detection methods) wherein the composition consistsessentially of a single species. A skilled artisan may purify apolypeptide of the invention using standard techniques for proteinpurification in light of the teachings herein. Purity of a polypeptidemay be determined by a number of methods known to those of skill in theart, including for example, amino-terminal amino acid sequence analysis,gel electrophoresis, mass-spectrometry analysis and the methodsdescribed in the Exemplification section herein.

The terms “recombinant protein” or “recombinant polypeptide” refer to apolypeptide which is produced by recombinant DNA techniques. An exampleof such techniques includes the case when DNA encoding the expressedprotein is inserted into a suitable expression vector which is in turnused to transform a host cell to produce the protein or polypeptideencoded by the DNA.

A “reference sequence” is a defined sequence used as a basis for asequence comparison; a reference sequence may be a subset of a largersequence, for example, as a segment of a full-length protein given in asequence listing such as SEQ ID NO: 2 or SEQ ID NO: 4, or may comprise acomplete protein sequence. Generally, a reference sequence is at least200, 300 or 400 nucleotides in length, frequently at least 600nucleotides in length, and often at least 800 nucleotides in length (orthe protein equivalent if it is shorter or longer in length). Becausetwo proteins may each (1) comprise a sequence (i.e., a portion of thecomplete protein sequence) that is similar between the two proteins, and(2) may further comprise a sequence that is divergent between the twoproteins, sequence comparisons between two (or more) proteins aretypically performed by comparing sequences of the two proteins over a“comparison window” to identify and compare local regions of sequencesimilarity.

The term “regulatory sequence” is a generic term used throughout thespecification to refer to polynucleotide sequences, such as initiationsignals, enhancers, regulators and promoters, that are necessary ordesirable to affect the expression of coding and non-coding sequences towhich they are operably linked. Exemplary regulatory sequences aredescribed in Goeddel; Gene Expression Technology: Methods in Enzymology,Academic Press, San Diego, Calif. (1990), and include, for example, theearly and late promoters of SV40, adenovirus or cytomegalovirusimmediate early promoter, the lac system, the trp system, the TAC or TRCsystem, T7 promoter whose expression is directed by T7 RNA polymerase,the major operator and promoter regions of phage lambda, the controlregions for fd coat protein, the promoter for 3-phosphoglycerate kinaseor other glycolytic enzymes, the promoters of acid phosphatase, e.g.,Pho5, the promoters of the yeast α-mating factors, the polyhedronpromoter of the baculovirus system and other sequences known to controlthe expression of genes of prokaryotic or eukaryotic cells or theirviruses, and various combinations thereof. The nature and use of suchcontrol sequences may differ depending upon the host organism. Inprokaryotes, such regulatory sequences generally include promoter,ribosomal binding site, and transcription termination sequences. Theterm “regulatory sequence” is intended to include, at a minimum,components whose presence may influence expression, and may also includeadditional components whose presence is advantageous, for example,leader sequences and fusion partner sequences. In certain embodiments,transcription of a polynucleotide sequence is under the control of apromoter sequence (or other regulatory sequence) which controls theexpression of the polynucleotide in a cell-type in which expression isintended. It will also be understood that the polynucleotide can beunder the control of regulatory sequences which are the same ordifferent from those sequences which control expression of thenaturally-occurring form of the polynucleotide.

The term “reporter gene” refers to a nucleic acid comprising anucleotide sequence encoding a protein that is readily detectable eitherby its presence or activity, including, but not limited to, luciferase,fluorescent protein (e.g., green fluorescent protein), chloramphenicolacetyl transferase, β-galactosidase, secreted placental alkalinephosphatase, β-lactamase, human growth hormone, and other secretedenzyme reporters. Generally, a reporter gene encodes a polypeptide nototherwise produced by the host cell, which is detectable by analysis ofthe cell(s), e.g., by the direct fluorometric, radioisotopic orspectrophotometric analysis of the cell(s) and preferably without theneed to kill the cells for signal analysis. In certain instances, areporter gene encodes an enzyme, which produces a change in fluorometricproperties of the host cell, which is detectable by qualitative,quantitative or semiquantitative function or transcriptional activation.Exemplary enzymes include esterases, β-lactamase, phosphatases,peroxidases, proteases (tissue plasminogen activator or urokinase) andother enzymes whose function may be detected by appropriate chromogenicor fluorogenic substrates known to those skilled in the art or developedin the future.

The term “sequence homology” refers to the proportion of base matchesbetween two nucleic acid sequences or the proportion of amino acidmatches between two amino acid sequences. When sequence homology isexpressed as a percentage, e.g., 50%, the percentage denotes theproportion of matches over the length of sequence from a desiredsequence (e.g., SEQ. ID NO: 1) that is compared to some other sequence.Gaps (in either of the two sequences) are permitted to maximizematching; gap lengths of 15 bases or less are usually used, 6 bases orless are used more frequently, with 2 bases or less used even morefrequently. The term “sequence identity” means that sequences areidentical (i.e., on a nucleotide-by-nucleotide basis for nucleic acidsor amino acid-by-amino acid basis for polypeptides) over a window ofcomparison. The term “percentage of sequence identity” is calculated bycomparing two optimally aligned sequences over the comparison window,determining the number of positions at which the identical amino acidsoccurs in both sequences to yield the number of matched positions,dividing the number of matched positions by the total number ofpositions in the comparison window, and multiplying the result by 100 toyield the percentage of sequence identity. Methods to calculate sequenceidentity are known to those of skill in the art and described in furtherdetail below.

The term “small molecule” refers to a compound, which has a molecularweight of less than about 5 kD, less than about 2.5 kD, less than about1.5 kD, or less than about 0.9 kD. Small molecules may be, for example,nucleic acids, peptides, polypeptides, peptide nucleic acids,peptidomimetics, carbohydrates, lipids or other organic (carboncontaining) or inorganic molecules. Many pharmaceutical companies haveextensive libraries of chemical and/or biological mixtures, oftenfungal, bacterial, or algal extracts, which can be screened with any ofthe assays of the invention. The term “small organic molecule” refers toa small molecule that is often identified as being an organic ormedicinal compound, and does not include molecules that are exclusivelynucleic acids, peptides or polypeptides.

The term “soluble” as used herein with reference to a polypeptide of theinvention or other protein, means that upon expression in cell culture,at least some portion of the polypeptide or protein expressed remains inthe cytoplasmic fraction of the cell and does not fractionate with thecellular debris upon lysis and centrifugation of the lysate. Solubilityof a polypeptide may be increased by a variety of art recognizedmethods, including fusion to a heterologous amino acid sequence,deletion of amino acid residues, amino acid substitution (e.g.,enriching the sequence with amino acid residues having hydrophilic sidechains), and chemical modification (e.g., addition of hydrophilicgroups). The solubility of polypeptides may be measured using a varietyof art recognized techniques, including, dynamic light scattering todetermine aggregation state, UV absorption, centrifugation to separateaggregated from non-aggregated material, and SDS gel electrophoresis(e.g., the amount of protein in the soluble fraction is compared to theamount of protein in the soluble and insoluble fractions combined). Whenexpressed in a host cell, the polypeptides of the invention may be atleast about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% ormore soluble, e.g., at least about 1%, 2%, 5%, 10%, 20%, 30%, 40%, 50%,60%, 70%, 80%, 90% or more of the total amount of protein expressed inthe cell is found in the cytoplasmic fraction. In certain embodiments, aone liter culture of cells expressing a polypeptide of the inventionwill produce at least about 0.1, 0.2, 0.5, 1, 2, 5, 10, 20, 30, 40, 50milligrams or more of soluble protein. In an exemplary embodiment, apolypeptide of the invention is at least about 10% soluble and willproduce at least about 1 milligram of protein from a one liter cellculture.

The term “specifically hybridizes” refers to detectable and specificnucleic acid binding. Polynucleotides, oligonucleotides and nucleicacids of the invention selectively hybridize to nucleic acid strandsunder hybridization and wash conditions that minimize appreciableamounts of detectable binding to nonspecific nucleic acids. Stringentconditions may be used to achieve selective hybridization conditions asknown in the art and discussed herein. Generally, the nucleic acidsequence homology between the polynucleotides, oligonucleotides, andnucleic acids of the invention and a nucleic acid sequence of interestwill be at least 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98%, 99%,or more. In certain instances, hybridization and washing conditions areperformed under stringent conditions according to conventionalhybridization procedures and as described further herein.

The terms “stringent conditions” or “stringent hybridization conditions”refer to conditions which promote specific hydribization between twocomplementary polynucleotide strands so as to form a duplex. Stringentconditions may be selected to be about 5° C. lower than the thermalmelting point (Tm) for a given polynucleotide duplex at a defined ionicstrength and pH. The length of the complementary polynucleotide strandsand their GC content will determine the Tm of the duplex, and thus thehybridization conditions necessary for obtaining a desired specificityof hybridization. The Tm is the temperature (under defined ionicstrength and pH) at which 50% of the a polynucleotide sequencehybridizes to a perfectly matched complementary strand. In certain casesit may be desirable to increase the stringency of the hybridizationconditions to be about equal to the Tm for a particular duplex.

A variety of techniques for estimating the Tm are available. Typically,G-C base pairs in a duplex are estimated to contribute about 3° C. tothe Tm, while A-T base pairs are estimated to contribute about 2° C., upto a theoretical maximum of about 80-100° C. However, more sophisticatedmodels of Tm are available in which G-C stacking interactions, solventeffects, the desired assay temperature and the like are taken intoaccount. For example, probes can be designed to have a dissociationtemperature (Td) of approximately 60° C., using the formula:Td=(((((3×#GC)+(2×#AT))×37)−562)/#bp)−5; where #GC, #AT, and #bp are thenumber of guanine-cytosine base pairs, the number of adenine-thyminebase pairs, and the number of total base pairs, respectively, involvedin the formation of the duplex.

Hybridization may be carried out in 5×SSC, 4×SSC, 3×SSC, 2×SSC, 1×SSC or0.2×SSC for at least about 1 hour, 2 hours, 5 hours, 12 hours, or 24hours. The temperature of the hybridization may be increased to adjustthe stringency of the reaction, for example, from about 25° C. (roomtemperature), to about 45° C., 50° C., 55° C., 60° C., or 65° C. Thehybridization reaction may also include another agent affecting thestringency, for example, hybridization conducted in the presence of 50%formamide increases the stringency of hybridization at a definedtemperature.

The hybridization reaction may be followed by a single wash step, or twoor more wash steps, which may be at the same or a different salinity andtemperature. For example, the temperature of the wash may be increasedto adjust the stringency from about 25° C. (room temperature), to about45° C., 50° C., 55° C., 60° C., 65° C., or higher. The wash step may beconducted in the presence of a detergent, e.g., 0.1 or 0.2% SDS. Forexample, hybridization may be followed by two wash steps at 65° C. eachfor about 20 minutes in 2×SSC, 0.1% SDS, and optionally two additionalwash steps at 65° C. each for about 20 minutes in 0.2×SSC, 0.1% SDS.

Exemplary stringent hybridization conditions include overnighthybridization at 65° C. in a solution comprising, or consisting of, 50%formamide, 10× Denhardt (0.2% Ficoll, 0.2% Polyvinylpyrrolidone, 0.2%bovine serum albumin) and 200 μg/ml of denatured carrier DNA, e.g.,sheared salmon sperm DNA, followed by two wash steps at 65° C. each forabout 20 minutes in 2×SSC, 0.1% SDS, and two wash steps at 65° C. eachfor about 20 minutes in 0.2×SSC, 0.1% SDS.

Hybridization may consist of hybridizing two nucleic acids in solution,or a nucleic acid in solution to a nucleic acid attached to a solidsupport, e.g., a filter. When one nucleic acid is on a solid support, aprehybridization step may be conducted prior to hybridization.Prehybridization may be carried out for at least about 1 hour, 3 hoursor 10 hours in the same solution and at the same temperature as thehybridization solution (without the complementary polynucleotidestrand).

Appropriate stringency conditions are known to those skilled in the artor may be determined experimentally by the skilled artisan. See, forexample, Current Protocols in Molecular Biology, John Wiley & Sons, N.Y.(1989), 6.3.1-12.3.6; Sambrook et al., 1989, Molecular Cloning, ALaboratory Manual, Cold Spring Harbor Press, N.Y; S. Agrawal (ed.)Methods in Molecular Biology, volume 20; Tijssen (1993) LaboratoryTechniques in biochemistry and molecular biology-hybridization withnucleic acid probes, e.g., part I chapter 2 “Overview of principles ofhybridization and the strategy of nucleic acid probe assays”, Elsevier,New York; and Tibanyenda, N. et al., Eur. J. Biochem. 139:19 (1984) andEbel, S. et al., Biochem. 31:12083 (1992).

As applied to proteins, the term “substantial identity” means that twoprotein sequences, when optimally aligned, such as by the programs GAPor BESTFIT using default gap weights, typically share at least about 70percent sequence identity, alternatively at least about 80, 85, 90, 95percent sequence identity or more. In certain instances, residuepositions that are not identical differ by conservative amino acidsubstitutions, which are described above.

The term “structural motif”, when used in reference to a polypeptide,refers to a polypeptide that, although it may have different amino acidsequences, may result in a similar structure, wherein by structure ismeant that the motif forms generally the same tertiary structure, orthat certain amino acid residues within the motif, or alternativelytheir backbone or side chains (which may or may not include the Ca atomsof the side chains) are positioned in a like relationship with respectto one another in the motif.

The term “test compound” refers to a molecule to be tested by one ormore screening method(s) as a putative modulator of a polypeptide of theinvention or other biological entity or process. A test compound isusually not known to bind to a target of interest. The term “controltest compound” refers to a compound known to bind to the target (e.g., aknown agonist, antagonist, partial agonist or inverse agonist). The term“test compound” does not include a chemical added as a control conditionthat alters the function of the target to determine signal specificityin an assay. Such control chemicals or conditions include chemicalsthat 1) nonspecifically or substantially disrupt protein structure(e.g., denaturing agents (e.g., urea or guanidinium), chaotropic agents,sulfhydryl reagents (e.g., dithiothreitol and β-mercaptoethanol), andproteases), 2) generally inhibit cell metabolism (e.g., mitochondrialuncouplers) and 3) non-specifically disrupt electrostatic or hydrophobicinteractions of a protein (e.g., high salt concentrations, or detergentsat concentrations sufficient to non-specifically disrupt hydrophobicinteractions). Further, the term “test compound” also does not includecompounds known to be unsuitable for a therapeutic use for a particularindication due to toxicity of the subject. In certain embodiments,various predetermined concentrations of test compounds are used forscreening such as 0.01 μM, 0.1 μM, 1.0 μM, and 10.0 μM. Examples of testcompounds include, but are not limited to, peptides, nucleic acids,carbohydrates, and small molecules. The term “novel test compound”refers to a test compound that is not in existence as of the filing dateof this application. In certain assays using novel test compounds, thenovel test compounds comprise at least about 50%, 75%, 85%, 90%, 95% ormore of the test compounds used in the assay or in any particular trialof the assay.

The term “therapeutically effective amount” refers to that amount of amodulator, drug or other molecule which is sufficient to effecttreatment when administered to a subject in need of such treatment. Thetherapeutically effective amount will vary depending upon the subjectand disease condition being treated, the weight and age of the subject,the severity of the disease condition, the manner of administration andthe like, which can readily be determined by one of ordinary skill inthe art.

The term “transfection” means the introduction of a nucleic acid, e.g.,an expression vector, into a recipient cell, which in certain instancesinvolves nucleic acid-mediated gene transfer. The term “transformation”refers to a process in which a cell's genotype is changed as a result ofthe cellular uptake of exogenous nucleic acid. For example, atransformed cell may express a recombinant form of a polypeptide of theinvention or antisense expression may occur from the transferred gene sothat the expression of a naturally-occurring form of the gene isdisrupted.

The term “transgene” means a nucleic acid sequence, which is partly orentirely heterologous to a transgenic animal or cell into which it isintroduced, or, is homologous to an endogenous gene of the transgenicanimal or cell into which it is introduced, but which is designed to beinserted, or is inserted, into the animal's genome in such a way as toalter the genome of the cell into which it is inserted (e.g., it isinserted at a location which differs from that of the natural gene orits insertion results in a knockout). A transgene may include one ormore regulatory sequences and any other nucleic acids, such as introns,that may be necessary for optimal expression.

The term “transgenic animal” refers to any animal, for example, a mouse,rat or other non-human mammal, a bird or an amphibian, in which one ormore of the cells of the animal contain heterologous nucleic acidintroduced by way of human intervention, such as by transgenictechniques well known in the art. The nucleic acid is introduced intothe cell, directly or indirectly, by way of deliberate geneticmanipulation, such as by microinjection or by infection with arecombinant virus. The term genetic manipulation does not includeclassical cross-breeding, or in vitro fertilization, but rather isdirected to the introduction of a recombinant DNA molecule. Thismolecule may be integrated within a chromosome, or it may beextrachromosomally replicating DNA. In the typical transgenic animalsdescribed herein, the transgene causes cells to express a recombinantform of a protein. However, transgenic animals in which the recombinantgene is silent are also contemplated.

The term “vector” refers to a nucleic acid capable of transportinganother nucleic acid to which it has been linked. One type of vectorwhich may be used in accord with the invention is an episome, i.e., anucleic acid capable of extra-chromosomal replication. Other vectorsinclude those capable of autonomous replication and expression ofnucleic acids to which they are linked. Vectors capable of directing theexpression of genes to which they are operatively linked are referred toherein as “expression vectors”. In general, expression vectors ofutility in recombinant DNA techniques are often in the form of“plasmids” which refer to circular double stranded DNA molecules which,in their vector form are not bound to the chromosome. In the presentspecification, “plasmid” and “vector” are used interchangeably as theplasmid is the most commonly used form of vector. However, the inventionis intended to include such other forms of expression vectors whichserve equivalent functions and which become known in the artsubsequently hereto.

Unless otherwise indicated, all numbers expressing quantities ofingredients, reaction conditions, and so forth used in the specificationand claims are to be understood as being modified in all instances bythe term “about.” Accordingly, unless indicated to the contrary, thenumerical parameters set forth in this specification and attached claimsare approximations that may vary depending upon the desired propertiessought to be obtained by the present invention.

2. Polypeptides of the Invention

The present invention makes available in a variety of embodimentssoluble, purified and/or isolated forms of the polypeptides of theinvention. Milligram quantities of an exemplary polypeptide of theinvention, SEQ ID NO: 4 (optionally with a tag, and optionally labeled),have been isolated in a highly purified form. The present inventionprovides for expressing and purifying polypeptides of the invention inquantities that equal or exceed the quantity of polypeptide(s) of theinvention expressed and purified as provided in the Exemplificationsection below (or smaller amount(s) thereof, such as 25%, 33%, 50% or75% of the amount(s) so expressed and/or purified).

In one aspect, the present invention contemplates an isolatedpolypeptide comprising (a) the amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4, (b) the amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4 with 1 to about 20 conservative amino acidsubstitutions, deletions or additions, (c) an amino acid sequence thatis at least 90% identical to SEQ ID NO: 2 or SEQ ID NO: 4 or (d) afunctional fragment of a polypeptide having an amino acid sequence setforth in (a), (b) or (c). In another aspect, the present inventioncontemplates a composition comprising such an isolated polypeptide andless than about 10%, or alternatively 5%, or alternatively 1%,contaminating biological macromolecules or polypeptides.

It may be the case that the amino acid sequence of SEQ ID NO: 4 differsfrom that of SEQ ID NO: 2 by one or more amino acids. SEQ ID NO: 4 isdetermined from the experimentally determined nucleic acid sequence SEDID NO: 3, and SEQ ID NO: 2 is determined from SEQ ID NO: 1, which isobtained as described in EXAMPLE 1. In such a case, the presentinvention contemplates the specific amino acid sequences of SEQ ID NO: 2and SEQ ID NO: 4, and variants thereof, as well as any differences (ifany) in the polypeptides of the invention based on those SEQ ID NOS andnucleic acid sequences encoding the same.

In certain embodiments, a polypeptide of the invention is a fusionprotein containing a domain which increases its solubility and/orfacilitates its purification, identification, detection, and/orstructural characterization. Exemplary domains, include, for example,glutathione S-transferase (GST), protein A, protein G,calmodulin-binding peptide, thioredoxin, maltose binding protein, HA,myc, poly arginine, poly His, poly His-Asp or FLAG fusion proteins andtags. Additional exemplary domains include domains that alter proteinlocalization in vivo, such as signal peptides, type III secretionsystem-targeting peptides, transcytosis domains, nuclear localizationsignals, etc. In various embodiments, a polypeptide of the invention maycomprise one or more heterologous fusions. Polypeptides may containmultiple copies of the same fusion domain or may contain fusions to twoor more different domains. The fusions may occur at the N-terminus ofthe polypeptide, at the C-terminus of the polypeptide, or at both the N-and C-terminus of the polypeptide. It is also within the scope of theinvention to include linker sequences between a polypeptide of theinvention and the fusion domain in order to facilitate construction ofthe fusion protein or to optimize protein expression or structuralconstraints of the fusion protein. In another embodiment, thepolypeptide may be constructed so as to contain protease cleavage sitesbetween the fusion polypeptide and polypeptide of the invention in orderto remove the tag after protein expression or thereafter. Examples ofsuitable endoproteases, include, for example, Factor Xa and TEVproteases.

In another embodiment, a polypeptide of the invention may be modified sothat its rate of traversing the cellular membrane is increased. Forexample, the polypeptide may be fused to a second peptide which promotes“transcytosis,” e.g., uptake of the peptide by cells. The peptide may bea portion of the HIV transactivator (TAT) protein, such as the fragmentcorresponding to residues 37-62 or 48-60 of TAT, portions which havebeen observed to be rapidly taken up by a cell in vitro (Green andLoewenstein, (1989) Cell 55:1179-1188). Alternatively, the internalizingpeptide may be derived from the Drosophila antennapedia protein, orhomologs thereof. The 60 amino acid long homeodomain of thehomeo-protein antennapedia has been demonstrated to translocate throughbiological membranes and can facilitate the translocation ofheterologous polypeptides to which it is coupled. Thus, polypeptides maybe fused to a peptide consisting of about amino acids 42-58 ofDrosophila antennapedia or shorter fragments for transcytosis (Derossiet al. (1996) J Biol Chem 271:18188-18193; Derossi et al. (1994) J BiolChem 269:10444-10450; and Perez et al. (1992) J Cell Sci 102:717-722).The transcytosis polypeptide may also be a non-naturally-occurringmembrane-translocating sequence (MTS), such as the peptide sequencesdisclosed in U.S. Pat. No. 6,248,558.

In another embodiment, a polypeptide of the invention is labeled with anisotopic label to facilitate its detection and or structuralcharacterization using nuclear magnetic resonance or another applicabletechnique. Exemplary isotopic labels include radioisotopic labels suchas, for example, potassium-40 (⁴⁰K), carbon-14 (¹⁴C), tritium (³H),sulphur-35 (³⁵S), phosphorus-32 (³²P), technetium-99m (^(99m)Tc),thallium-201 (²⁰¹Tl), gallium-67 (⁶⁷ Ga), indium-111 (¹¹¹In), iodine-123(¹²³I), iodine-131 (¹³¹I), yttrium-90 (⁹⁰Y), samarium-153 (¹⁵³Sm),rhenium-186 (¹⁸⁶ Re), rhenium-188 (¹⁸⁸Re), dysprosium-165 (¹⁶⁵Dy) andholmium-166 (¹⁶⁶Ho). The isotopic label may also be an atom with nonzero nuclear spin, including, for example, hydrogen-1 (¹H), hydrogen-2(²H), hydrogen-3 (³H), phosphorous-31 (³¹P), sodium-23 (²³Na),nitrogen-14 (¹⁴N), nitrogen-15 (¹⁵N), carbon-13 (¹³C) and fluorine-19(¹⁹F). In certain embodiments, the polypeptide is uniformly labeled withan isotopic label, for example, wherein at least 50%, 70%, 80%, 90%,95%, or 98% of the possible labels in the polypeptide are labeled, e.g.,wherein at least 50%, 70%, 80%, 90%, 95%, or 98% of the nitrogen atomsin the polypeptide are ¹⁵N, and/or wherein at least 50%, 70%, 80%, 90%,95%, or 98% of the carbon atoms in the polypeptide are ¹³C, and/orwherein at least 50%, 70%, 80%, 90%, 95%, or 98% of the hydrogen atomsin the polypeptide are 2H. In other embodiments, the isotopic label islocated in one or more specific locations within the polypeptide, forexample, the label may be specifically incorporated into one or more ofthe leucine residues of the polypeptide. The invention also encompassesthe embodiment wherein a single polypeptide comprises two, three or moredifferent isotopic labels, for example, the polypeptide comprises both¹⁵N and ¹³C labeling.

In yet another embodiment, the polypeptides of the invention are labeledto facilitate structural characterization using x-ray crystallography oranother applicable technique. Exemplary labels include heavy atom labelssuch as, for example, cobalt, selenium, krypton, bromine, strontium,molybdenum, ruthenium, rhodium, palladium, silver, cadmium, tin, iodine,xenon, barium, lanthanum, cerium, praseodymium, neodymium, samarium,europium, gadolinium, terbium, dysprosium, holmium, erbium, thulium,ytterbium, lutetium, tantalum, tungsten, rhenium, osmium, iridium,platinum, gold, mercury, thallium, lead, thorium and uranium. In anexemplary embodiment, the polypeptide is labeled with seleno-methionine.

A variety of methods are available for preparing a polypeptide with alabel, such as a radioisotopic label or heavy atom label. For example,in one such method, an expression vector comprising a nucleic acidencoding a polypeptide is introduced into a host cell, and the host cellis cultured in a cell culture medium in the presence of a source of thelabel, thereby generating a labeled polypeptide. As indicated above, theextent to which a polypeptide may be labeled may vary.

In still another embodiment, the polypeptides of the invention arelabeled with a fluorescent label to facilitate their detection,purification, or structural characterization. In an exemplaryembodiment, a polypeptide of the invention is fused to a heterologouspolypeptide sequence which produces a detectable fluorescent signal,including, for example, green fluorescent protein (GFP), enhanced greenfluorescent protein (EGFP), Renilla Reniformis green fluorescentprotein, GFPmut2, GFPuv4, enhanced yellow fluorescent protein (EYFP),enhanced cyan fluorescent protein (ECFP), enhanced blue fluorescentprotein (EBFP), citrine and red fluorescent protein from discosoma(dsRED).

In other embodiments, the invention provides for polypeptides of theinvention immobilized onto a solid surface, including, microtiterplates, slides, beads, films, etc. The polypeptides of the invention maybe immobilized onto a “chip” as part of an array. An array, having aplurality of addresses, may comprise one or more polypeptides of theinvention in one or more of those addresses. In one embodiment, the chipcomprises one or more polypeptides of the invention as part of an arrayof E. faecalis polypeptide sequences.

In other embodiments, the invention provides for polypeptides of theinvention immobilized onto a solid surface, including, plates,microtiter plates, slides, beads, particles, spheres, films, strands,precipitates, gels, sheets, tubing, containers, capillaries, pads,slices, etc. The polypeptides of the invention may be immobilized onto a“chip” as part of an array. An array, having a plurality of addresses,may comprise one or more polypeptides of the invention in one or more ofthose addresses. In one embodiment, the chip comprises one or morepolypeptides of the invention as part of an array that contains at leastsome polypeptide sequences from E. faecalis.

In still other embodiments, the invention comprises the polypeptidesequences of the invention in computer readable format. The inventionalso encompasses a database comprising the polypeptide sequences of theinvention.

In other embodiments, the invention relates to the polypeptides of theinvention contained within a vessels useful for manipulation of thepolypeptide sample. For example, the polypeptides of the invention maybe contained within a microtiter plate to facilitate detection,screening or purification of the polypeptide. The polypeptides may alsobe contained within a syringe as a container suitable for administeringthe polypeptide to a subject in order to generate antibodies or as partof a vaccination regimen. The polypeptides may also be contained withinan NMR tube in order to enable characterization by nuclear magneticresonance techniques.

In still other embodiments, the invention relates to a crystallizedpolypeptide of the invention and crystallized polypeptides which havebeen mounted for examination by x-ray crystallography as describedfurther below. In certain instances, a polypeptide of the invention incrystal form may be single crystals of various dimensions (e.g.,micro-crystals) or may be an aggregate of crystalline material. Inanother aspect, the present invention contemplates a crystallizedcomplex including a polypeptide of the invention and one or more of thefollowing: a co-factor (such as a salt, metal, nucleotide,oligonucleotide or polypeptide), a modulator, or a small molecule. Inanother aspect, the present invention contemplates a crystallizedcomplex including a polypeptide of the invention and any other moleculeor atom (such as a metal ion) that associates with the polypeptide invivo.

In certain embodiments, polypeptides of the invention may be synthesizedchemically, ribosomally in a cell free system, or ribosomally within acell. Chemical synthesis of polypeptides of the invention may be carriedout using a variety of art recognized methods, including stepwise solidphase synthesis, semi-synthesis through the conformationally-assistedre-ligation of peptide fragments, enzymatic ligation of cloned orsynthetic peptide segments, and chemical ligation. Native chemicalligation employs a chemoselective reaction of two unprotected peptidesegments to produce a transient thioester-linked intermediate. Thetransient thioester-linked intermediate then spontaneously undergoes arearrangement to provide the full length ligation product having anative peptide bond at the ligation site. Full length ligation productsare chemically identical to proteins produced by cell free synthesis.Full length ligation products may be refolded and/or oxidized, asallowed, to form native disulfide-containing protein molecules. (seee.g., U.S. Pat. Nos. 6,184,344 and 6,174,530; and T. W. Muir et al.,Curr. Opin. Biotech. (1993): vol. 4, p 420; M. Miller, et al., Science(1989): vol. 246, p 1149; A. Wlodawer, et al., Science (1989): vol. 245,p 616; L. H. Huang, et al., Biochemistry (1991): vol. 30, p 7402; M.Schnolzer, et al., Int. J. Pept. Prot. Res. (1992): vol. 40, p 180-193;K. Rajarathnam, et al., Science (1994): vol. 264, p 90; R. E. Offord,“Chemical Approaches to Protein Engineering”, in Protein Design and theDevelopment of New therapeutics and Vaccines, J. B. Hook, G. Poste,Eds., (Plenum Press, New York, 1990) pp. 253-282; C. J. A. Wallace, etal., J. Biol. Chem. (1992): vol. 267, p 3852; L. Abrahmsen, et al.,Biochemistry (1991): vol. 30, p 4151; T. K. Chang, et al., Proc. Natl.Acad. Sci. USA (1994) 91: 12544-12548; M. Schnlzer, et al., Science(1992): vol., 3256, p 221; and K. Akaji, et al., Chem. Pharm. Bull.(Tokyo) (1985) 33: 184).

In certain embodiments, it may be advantageous to providenaturally-occurring or experimentally-derived homologs of a polypeptideof the invention. Such homologs may function in a limited capacity as amodulator to promote or inhibit a subset of the biological activities ofthe naturally-occurring form of the polypeptide. Thus, specificbiological effects may be elicited by treatment with a homolog oflimited function, and with fewer side effects relative to treatment withagonists or antagonists which are directed to all of the biologicalactivities of a polypeptide of the invention. For instance, antagonistichomologs may be generated which interfere with the ability of thewild-type polypeptide of the invention to associate with certainproteins, but which do not substantially interfere with the formation ofcomplexes between the native polypeptide and other cellular proteins.

Another aspect of the invention relates to polypeptides derived from thefull-length polypeptides of the invention. Isolated peptidyl portions ofthose polypeptides may be obtained by screening polypeptidesrecombinantly produced from the corresponding fragment of the nucleicacid encoding such polypeptides. In addition, fragments may bechemically synthesized using techniques known in the art such asconventional Merrifield solid phase f-Moc or t-Boc chemistry. Forexample, proteins may be arbitrarily divided into fragments of desiredlength with no overlap of the fragments, or may be divided intooverlapping fragments of a desired length. The fragments may be produced(recombinantly or by chemical synthesis) and tested to identify thosepeptidyl fragments having a desired property, for example, thecapability of functioning as a modulator of the polypeptides of theinvention. In an illustrative embodiment, peptidyl portions of a proteinof the invention may be tested for binding activity, as well asinhibitory ability, by expression as, for example, thioredoxin fusionproteins, each of which contains a discrete fragment of a protein of theinvention (see, for example, U.S. Pat. Nos. 5,270,181 and 5,292,646; andPCT publication WO94/02502).

In another embodiment, truncated polypeptides may be prepared. Truncatedpolypeptides have from 1 to 20 or more amino acid residues removed fromeither or both the N- and C-termini. Such truncated polypeptides mayprove more amenable to expression, purification or characterization thanthe full-length polypeptide. For example, truncated polypeptides mayprove more amenable than the full-length polypeptide to crystallization,to yielding high quality diffracting crystals or to yielding an HSQCspectrum with high intensity peaks and minimally overlapping peaks. Inaddition, the use of truncated polypeptides may also identify stable andactive domains of the full-length polypeptide that may be more amenableto characterization.

It is also possible to modify the structure of the polypeptides of theinvention for such purposes as enhancing therapeutic or prophylacticefficacy, or stability (e.g., ex vivo shelf life, resistance toproteolytic degradation in vivo, etc.). Such modified polypeptides, whendesigned to retain at least one activity of the naturally-occurring formof the protein, are considered “functional equivalents” of thepolypeptides described in more detail herein. Such modified polypeptidesmay be produced, for instance, by amino acid substitution, deletion, oraddition, which substitutions may consist in whole or part byconservative amino acid substitutions.

For instance, it is reasonable to expect that an isolated conservativeamino acid substitution, such as replacement of a leucine with anisoleucine or valine, an aspartate with a glutamate, a threonine with aserine, will not have a major affect on the biological activity of theresulting molecule. Whether a change in the amino acid sequence of apolypeptide results in a functional homolog may be readily determined byassessing the ability of the variant polypeptide to produce a responsesimilar to that of the wild-type protein. Polypeptides in which morethan one replacement has taken place may readily be tested in the samemanner.

This invention further contemplates a method of generating sets ofcombinatorial mutants of polypeptides of the invention, as well astruncation mutants, and is especially useful for identifying potentialvariant sequences (e.g. homologs). The purpose of screening suchcombinatorial libraries is to generate, for example, homologs which maymodulate the activity of a polypeptide of the invention, oralternatively, which possess novel activities altogether.Combinatorially-derived homologs may be generated which have a selectivepotency relative to a naturally-occurring protein. Such homologs may beused in the development of therapeutics.

Likewise, mutagenesis may give rise to homologs which have intracellularhalf-lives dramatically different than the corresponding wild-typeprotein. For example, the altered protein may be rendered either morestable or less stable to proteolytic degradation or other cellularprocess which result in destruction of, or otherwise inactivation of theprotein. Such homologs, and the genes which encode them, may be utilizedto alter protein expression by modulating the half-life of the protein.As above, such proteins may be used for the development of therapeuticsor treatment.

In similar fashion, protein homologs may be generated by the presentcombinatorial approach to act as antagonists, in that they are able tointerfere with the activity of the corresponding wild-type protein.

In a representative embodiment of this method, the amino acid sequencesfor a population of protein homologs are aligned, preferably to promotethe highest homology possible. Such a population of variants mayinclude, for example, homologs from one or more species, or homologsfrom the same species but which differ due to mutation. Amino acidswhich appear at each position of the aligned sequences are selected tocreate a degenerate set of combinatorial sequences. In certainembodiments, the combinatorial library is produced by way of adegenerate library of genes encoding a library of polypeptides whicheach include at least a portion of potential protein sequences. Forinstance, a mixture of synthetic oligonucleotides may be enzymaticallyligated into gene sequences such that the degenerate set of potentialnucleotide sequences are expressible as individual polypeptides, oralternatively, as a set of larger fusion proteins (e.g. for phagedisplay).

There are many ways by which the library of potential homologs may begenerated from a degenerate oligonucleotide sequence. Chemical synthesisof a degenerate gene sequence may be carried out in an automatic DNAsynthesizer, and the synthetic genes may then be ligated into anappropriate vector for expression. One purpose of a degenerate set ofgenes is to provide, in one mixture, all of the sequences encoding thedesired set of potential protein sequences. The synthesis of degenerateoligonucleotides is well known in the art (see for example, Narang, S A(1983) Tetrahedron 39:3; Itakura et al., (1981) Recombinant DNA, Proc.3rd Cleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam:Elsevier pp. 273-289; Itakura et al., (1984) Annu. Rev. Biochem. 53:323;Itakura et al., (1984) Science 198:1056; Ike et al., (1983) Nucleic AcidRes. 11:477). Such techniques have been employed in the directedevolution of other proteins (see, for example, Scott et al., (1990)Science 249:386-390; Roberts et al., (1992) PNAS USA 89:2429-2433;Devlin et al., (1990) Science 249: 404-406; Cwirla et al., (1990) PNASUSA 87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and5,096,815).

Alternatively, other forms of mutagenesis may be utilized to generate acombinatorial library. For example, protein homologs (both agonist andantagonist forms) may be generated and isolated from a library byscreening using, for example, alanine scanning mutagenesis and the like(Ruf et al., (1994) Biochemistry 33:1565-1572; Wang et al., (1994) J.Biol. Chem. 269:3095-3099; Balint et al., (1993) Gene 137:109-118;Grodberg et al., (1993) Eur. J. Biochem. 218:597-601; Nagashima et al.,(1993) J. Biol. Chem. 268:2888-2892; Lowman et al., (1991) Biochemistry30:10832-10838; and Cunningham et al., (1989) Science 244:1081-1085), bylinker scanning mutagenesis (Gustin et al., (1993) Virology 193:653-660;Brown et al., (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al.,(1982) Science 232:316); by saturation mutagenesis (Meyers et al.,(1986) Science 232:613); by PCR mutagenesis (Leung et al., (1989) MethodCell Mol Biol 1:11-19); or by random mutagenesis (Miller et al., (1992)A Short Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor,N.Y.; and Greener et al., (1994) Strategies in Mol Biol 7:32-34). Linkerscanning mutagenesis, particularly in a combinatorial setting, is anattractive method for identifying truncated forms of proteins that arebioactive.

A wide range of techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations andtruncations, and for screening cDNA libraries for gene products having acertain property. Such techniques will be generally adaptable for rapidscreening of the gene libraries generated by the combinatorialmutagenesis of protein homologs. The most widely used techniques forscreening large gene libraries typically comprises cloning the genelibrary into replicable expression vectors, transforming appropriatecells with the resulting library of vectors, and expressing thecombinatorial genes under conditions in which detection of a desiredactivity facilitates relatively easy isolation of the vector encodingthe gene whose product was detected. Each of the illustrative assaysdescribed below are amenable to high throughput analysis as necessary toscreen large numbers of degenerate sequences created by combinatorialmutagenesis techniques.

In an illustrative embodiment of a screening assay, candidatecombinatorial gene products are displayed on the surface of a cell andthe ability of particular cells or viral particles to bind to thecombinatorial gene product is detected in a “panning assay”. Forinstance, the gene library may be cloned into the gene for a surfacemembrane protein of a bacterial cell (Ladner et al., WO 88/06630; Fuchset al., (1991) Bio/Technology 9:1370-1371; and Goward et al., (1992)TIBS 18:136-140), and the resulting fusion protein detected by panning,e.g. using a fluorescently labeled molecule which binds the cell surfaceprotein, e.g. FITC-substrate, to score for potentially functionalhomologs. Cells may be visually inspected and separated under afluorescence microscope, or, when the morphology of the cell permits,separated by a fluorescence-activated cell sorter. This method may beused to identify substrates or other polypeptides that can interact witha polypeptide of the invention.

In similar fashion, the gene library may be expressed as a fusionprotein on the surface of a viral particle. For instance, in thefilamentous phage system, foreign peptide sequences may be expressed onthe surface of infectious phage, thereby conferring two benefits. First,because these phage may be applied to affinity matrices at very highconcentrations, a large number of phage may be screened at one time.Second, because each infectious phage displays the combinatorial geneproduct on its surface, if a particular phage is recovered from anaffinity matrix in low yield, the phage may be amplified by anotherround of infection. The group of almost identical E. coli filamentousphages M13, fd, and f1 are most often used in phage display libraries,as either of the phage gIII or gVIII coat proteins may be used togenerate fusion proteins without disrupting the ultimate packaging ofthe viral particle (Ladner et al., PCT publication WO 90/02909; Garrardet al., PCT publication WO 92/09690; Marks et al., (1992) J. Biol. Chem.267:16007-16010; Griffiths et al., (1993) EMBO J. 12:725-734; Clacksonet al., (1991) Nature 352:624-628; and Barbas et al., (1992) PNAS USA89:4457-4461). Other phage coat proteins may be used as appropriate.

The invention also provides for reduction of the polypeptides of theinvention to generate mimetics, e.g. peptide or non-peptide agents,which are able to mimic binding of the authentic protein to anothercellular partner. Such mutagenic techniques as described above, as wellas the thioredoxin system, are also particularly useful for mapping thedeterminants of a protein which participates in a protein-proteininteraction with another protein. To illustrate, the critical residuesof a protein which are involved in molecular recognition of a substrateprotein may be determined and used to generate peptidomimetics that maybind to the substrate protein. The peptidomimetic may then be used as aninhibitor of the wild-type protein by binding to the substrate andcovering up the critical residues needed for interaction with thewild-type protein, thereby preventing interaction of the protein and thesubstrate. By employing, for example, scanning mutagenesis to map theamino acid residues of a protein which are involved in binding asubstrate polypeptide, peptidomimetic compounds may be generated whichmimic those residues in binding to the substrate. For instance,non-hydrolyzable peptide analogs of such residues may be generated usingbenzodiazepine (e.g., see Freidinger et al., in Peptides: Chemistry andBiology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands,1988), azepine (e.g., see Huffman et al., in Peptides: Chemistry andBiology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands,1988), substituted gamma lactam rings (Garvey et al., in Peptides:Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,Netherlands, 1988), keto-methylene pseudopeptides (Ewenson et al.,(1986) J. Med. Chem. 29:295; and Ewenson et al., in Peptides: Structureand Function (Proceedings of the 9th American Peptide Symposium) PierceChemical Co. Rockland, Ill., 1985), β-turn dipeptide cores (Nagai etal., (1985) Tetrahedron Lett 26:647; and Sato et al., (1986) J Chem SocPerkin Trans 1:1231), and β-aminoalcohols (Gordon et al., (1985) BiochemBiophys Res Commun 126:419; and Dann et al., (1986) Biochem Biophys ResCommun 134:71).

The activity of a polypeptide of the invention may be identified and/orassayed using a variety of methods well known to the skilled artisan.For example, information about the activity of non-essential genes maybe assayed by creating a null mutant strain of bacteria expressing amutant form of, or lacking expression of, a protein of interest. Theresulting phenotype of the null mutant strain may provide informationabout the activity of the mutated gene product. Essential genes may bestudied by creating a bacterial strain with a conditional mutation inthe gene of interest. The bacterial strain may be grown under permissiveand non-permissive conditions and the change in phenotype under thenon-permissive conditions may be used to identify and/or assay theactivity of the gene product.

In an alternative embodiment, the activity of a protein may be assayedusing an appropriate substrate or binding partner or other reagentsuitable to test for the suspected activity. For catalytic activity, theassay is typically designed so that the enzymatic reaction produces adetectable signal. For example, mixture of a kinase with a substrate inthe presence of ³²P will result in incorporation of the ³²P into thesubstrate. The labeled substrate may then be separated from the free ³²Pand the presence and/or amount of radiolabeled substrate may be detectedusing a scintillation counter or a phosphorimager. Similar assays may bedesigned to identify and/or assay the activity of a wide variety ofenzymatic activities. Based on the teachings herein, the skilled artisanwould readily be able to develop an appropriate assay for a polypeptideof the invention.

In another embodiment, the activity of a polypeptide of the inventionmay be determined by assaying for the level of expression of RNA and/orprotein molecules. Transcription levels may be determined, for example,using Northern blots, hybridization to an oligonucleotide array or byassaying for the level of a resulting protein product. Translationlevels may be determined, for example, using Western blotting or byidentifying a detectable signal produced by a protein product (e.g.,fluorescence, luminescence, enzymatic activity, etc.). Depending on theparticular situation, it may be desirable to detect the level oftranscription and/or translation of a single gene or of multiple genes.

Alternatively, it may be desirable to measure the overall rate of DNAreplication, transcription and/or translation in a cell. In general thismay be accomplished by growing the cell in the presence of a detectablemetabolite which is incorporated into the resultant DNA, RNA, or proteinproduct. For example, the rate of DNA synthesis may be determined bygrowing cells in the presence of BrdU which is incorporated into thenewly synthesized DNA. The amount of BrdU may then be determinedhistochemically using an anti-BrdU antibody.

In general, the biological activity of a polypeptide encoded by SEQ IDNO. 2, and possibly other polypeptides of the invention, is guanylatekinase, having the gene designation of gmk. The foregoing annotationswere determined in accordance with the procedure described in EXAMPLE17. This functionality asignment has been confirmed by completion of theX-ray structure of a polypeptide of the invention, as described in moredetail below. In one aspect, the present invention contemplates apolypeptide having biological activity, or is a component of a proteincomplex having biological activity, substantially similar to oridentical to guanylate kinase. Alternatively, the polypeptide catalyzes,or is a component of a protein complex that catalyzes, a reaction thatis substantially the same type of, or is the same as, the reactioncatalyzed by guanylate kinase. Other biological activities ofpolypeptides of the invention are described herein, or will bereasonably apparent to those skilled in the art in light of the presentdisclosure.

Guanylate kinase is thought to be a cytoplasmic enzyme that catalysesthe reaction between ATP and GMP, which produces ADP and GDP.Alternatively, dGMP may act as an acceptor in this reaction and dATP mayact as the donor. Guanylate kinase is essential for the recycling of GMPand thus, indirectly, cGMP, and therefore is a target of interest.

In E. coli, unlike its eukaryotic counterpart, guanylate kinase is knownto exist as a homotetramer in low ionic conditions, while under highionic conditions, it exists as a homodimer. Guanylate kinase has beensequenced as part of a number of bacterial genomes, some of whichinclude: B. aphidicola, B. halodurans, B. subtilis, C. crescentus, C.jejuni, C. muridarum, C. pneumoniae, C. trachomatis, D. radiodurans, H.pylori J99, E. coli, H. influenzae, L. lactis, M. gallisepticum, M.genitalium, M. leprae, M. pneumoniae, M. tuberculosis, N. meningitidis,P. aeruginosa, P. multocida, R. prowazekii, S. coelicolor, S.typhimurium, T. maritima, U. parvum, V. cholerae, and X. fastidiosa.

A number of x-ray crystallography studies of guanylate kinase have beenperformed including the enzyme from S. cerevisiae and the enzyme from S.cerevisiae with its substrate, GMP, at 2.0 and 1.9 angstrom-resolution.The secondary structure of S. cerevisiae guanylate kinase has also beenstudied utilizing circular dichroism spectroscopy. In addition, ¹H NMRstudies have been conducted on guanylate kinase from S. cerevisiae todetermine the N-terminal blocking group as well as to study thesteady-state kinetic parameters for both forward and reverse reactions.

Guanylate kinase is believed to be involved in nucleotide biosynthesisand the recycling mechanism of guanosine monophosphate. If the pathwayof this enzyme is blocked or inhibited, nucleotides cannot be reused bya bacterium and thus proteins cannot be produced by this organism.Accordingly, the targets are promising drug targets Alternatively, theactions of guanylate kinase may be utilized by a drug to end DNAsynthesis by a virus or bacterium. The drugs Valacyclovir and Acyclovir(Zovirax) have been developed to inhibit DNA synthesis in this lattercontext for the treatment of herpes zoster in immunocompetent patientsas well as herpes genitalis, and is currently under investigation forthe treatment of CMV prophylaxis in HIV-infected and organ and bonemarrow transplant patients. In vivo, Valacyclovir is converted toAcyclovir, which is then converted into a monophosphate, then into adiphosphate by guanylate kinase, and then into a triphosphate by variousenzymes. In the end, Acyclovir triphosphate inhibits viral DNApolymerase because it is a chain terminator.

For all of the foregoing reasons, the polypeptides of the presentinvention are potentially valuable targets for therapeutics anddiagnostics.

3. Nucleic Acids of the Invention

One aspect of the invention pertains to isolated nucleic acids of theinvention. For example, the present invention contemplates an isolatednucleic acid comprising (a) the nucleotide sequence of SEQ ID NO: 1 orSEQ ID NO: 3, (b) a nucleotide sequence at least 80% identical to SEQ IDNO: 1 or SEQ ID NO: 3, (c) a nucleotide sequence that hybridizes understringent conditions to SEQ ID NO: 1 or SEQ ID NO: 3, or (d) thecomplement of the nucleotide sequence of (a), (b) or (c). In certainembodiments, nucleic acids of the invention may be labeled, with forexample, a radioactive, chemiluminescent or fluorescent label.

It may be that case that the nucleic acid sequence of SEQ ID NO: 3differs from that of SEQ ID NO: 1 by one or more nucleic acid residues.SEQ ID NO: 3 is determined experimetally, and SEQ ID NO: 1 obtained asdescribed in EXAMPLE 1. In such a case, the present inventioncontemplates the specific nucleic acid sequences of SEQ ID NO: 1 and SEQID NO: 3, and variants thereof, as well as any differences in theapplicable amino acid sequences encoded thereby.

In another aspect, the present invention contemplates an isolatednucleic acid that specifically hybridizes under stringent conditions toat least ten nucleotides of SEQ ID NO: 1 or SEQ ID NO: 3, or thecomplement thereof, which nucleic acid can specifically detect oramplify SEQ ID NO: 1 or SEQ ID NO: 3, or the complement thereof. In yetanother aspect, the present invention contemplates such an isolatednucleic acid comprising a nucleotide sequence encoding a fragment of SEQID NO: 2 or SEQ ID NO: 4 at least 8 residues in length. The presentinvention further contemplates a method of hybridizing anoligonucleotide with a nucleic acid of the invention comprising: (a)providing a single-stranded oligonucleotide at least eight nucleotidesin length, the oligonucleotide being complementary to a portion of anucleic acid of the invention; and (b) contacting the oligonucleotidewith a sample comprising a nucleic acid of the acid under conditionsthat permit hybridization of the oligonucleotide with the nucleic acidof the invention.

Isolated nucleic acids which differ from the nucleic acids of theinvention due to degeneracy in the genetic code are also within thescope of the invention. For example, a number of amino acids aredesignated by more than one triplet. Codons that specify the same aminoacid, or synonyms (for example, CAU and CAC are synonyms for histidine)may result in “silent” mutations which do not affect the amino acidsequence of the protein. However, it is expected that DNA sequencepolymorphisms that do lead to changes in the amino acid sequences of thepolypeptides of the invention will exist. One skilled in the art willappreciate that these variations in one or more nucleotides (from lessthan 1% up to about 3 or 5% or possibly more of the nucleotides) of thenucleic acids encoding a particular protein of the invention may existamong a given species due to natural allelic variation. Any and all suchnucleotide variations and resulting amino acid polymorphisms are withinthe scope of this invention.

Bias in codon choice within genes in a single species appears related tothe level of expression of the protein encoded by that gene.Accordingly, the invention encompasses nucleic acid sequences which havebeen optimized for improved expression in a host cell by altering thefrequency of codon usage in the nucleic acid sequence to approach thefrequency of preferred codon usage of the host cell. Due to codondegeneracy, it is possible to optimize the nucleotide sequence withoutaffecting the amino acid sequence of an encoded polypeptide.Accordingly, the instant invention relates to any nucleotide sequencethat encodes all or a substantial portion of the amino acid sequence setforth in SEQ ID NO: 2, SEQ ID NO: 4 or other polypeptides of theinvention.

The present invention pertains to nucleic acids encoding proteinsderived from E. faecalis and which have amino acid sequencesevolutionarily related to a polypeptide of the invention, wherein“evolutionarily related to”, refers to proteins having different aminoacid sequences which have arisen naturally (e.g. by allelic variance orby differential splicing), as well as mutational variants of theproteins of the invention which are derived, for example, bycombinatorial mutagenesis.

Fragments of the polynucleotides of the invention encoding abiologically active portion of the subject polypeptides are also withinthe scope of the invention. As used herein, a fragment of a nucleic acidof the invention encoding an active portion of a polypeptide of theinvention refers to a nucleotide sequence having fewer nucleotides thanthe nucleotide sequence encoding the full length amino acid sequence ofa polypeptide of the invention, for example, SEQ ID NO: 2 or SEQ ID NO:4, and which encodes a polypeptide which retains at least a portion of abiological activity of the full-length protein as defined herein, oralternatively, which is functional as a modulator of the biologicalactivity of the full-length protein. For example, such fragments includea polypeptide containing a domain of the full-length protein from whichthe polypeptide is derived that mediates the interaction of the proteinwith another molecule (e.g., polypeptide, DNA, RNA, etc.). In anotherembodiment, the present invention contemplates an isolated nucleic acidthat encodes a polypeptide having a biological activity of a proteinhaving the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO:4, or alternatively biological activity of guanylate kinase.

Nucleic acids within the scope of the invention may also contain linkersequences, modified restriction endonuclease sites and other sequencesuseful for molecular cloning, expression or purification of suchrecombinant polypeptides.

A nucleic acid encoding a polypeptide of the invention may be obtainedfrom mRNA or genomic DNA from any organism in accordance with protocolsdescribed herein, as well as those generally known to those skilled inthe art. A cDNA encoding a polypeptide of the invention, for example,may be obtained by isolating total mRNA from an organism, e.g. abacteria, virus, mammal, etc. Double stranded cDNAs may then be preparedfrom the total mRNA, and subsequently inserted into a suitable plasmidor bacteriophage vector using any one of a number of known techniques. Agene encoding a polypeptide of the invention may also be cloned usingestablished polymerase chain reaction techniques in accordance with thenucleotide sequence information provided by the invention. In oneaspect, the present invention contemplates a method for amplification ofa nucleic acid of the invention, or a fragment thereof, comprising: (a)providing a pair of single stranded oligonucleotides, each of which isat least eight nucleotides in length, complementary to sequences of anucleic acid of the invention, and wherein the sequences to which theoligonucleotides are complementary are at least ten nucleotides apart;and (b) contacting the oligonucleotides with a sample comprising anucleic acid comprising the nucleic acid of the invention underconditions which permit amplification of the region located between thepair of oligonucleotides, thereby amplifying the nucleic acid.

Another aspect of the invention relates to the use of nucleic acids ofthe invention in “antisense therapy”. As used herein, antisense therapyrefers to administration or in situ generation of oligonucleotide probesor their derivatives which specifically hybridize or otherwise bindunder cellular conditions with the cellular mRNA and/or genomic DNAencoding one of the polypeptides of the invention so as to inhibitexpression of that polypeptide, e.g. by inhibiting transcription and/ortranslation. The binding may be by conventional base paircomplementarity, or, for example, in the case of binding to DNAduplexes, through specific interactions in the major groove of thedouble helix. In general, antisense therapy refers to the range oftechniques generally employed in the art, and includes any therapy whichrelies on specific binding to oligonucleotide sequences.

An antisense construct of the present invention may be delivered, forexample, as an expression plasmid which, when transcribed in the cell,produces RNA which is complementary to at least a unique portion of themRNA which encodes a polypeptide of the invention. Alternatively, theantisense construct may be an oligonucleotide probe which is generatedex vivo and which, when introduced into the cell causes inhibition ofexpression by hybridizing with the mRNA and/or genomic sequencesencoding a polypeptide of the invention. Such oligonucleotide probes maybe modified oligonucleotides which are resistant to endogenousnucleases, e.g. exonucleases and/or endonucleases, and are thereforestable in vivo. Exemplary nucleic acid molecules for use as antisenseoligonucleotides are phosphoramidate, phosphothioate andmethylphosphonate analogs of DNA (see also U.S. Pat. Nos. 5,176,996;5,264,564; and 5,256,775). Additionally, general approaches toconstructing oligomers useful in antisense therapy have been reviewed,for example, by van der Krol et al., (1988) Biotechniques 6:958-976; andStein et al., (1988) Cancer Res 48:2659-2668.

In a further aspect, the invention provides double stranded smallinterfering RNAs (siRNAs), and methods for administering the same.siRNAs decrease or block gene expression. While not wishing to be boundby theory, it is generally thought that siRNAs inhibit gene expressionby mediating sequence specific mRNA degradation. RNA interference (RNAi)is the process of sequence-specific, post-transcriptional genesilencing, particularly in animals and plants, initiated bydouble-stranded RNA (dsRNA) that is homologous in sequence to thesilenced gene (Elbashir et al. Nature 2001; 411(6836): 494-8).Accordingly, it is understood that siRNAs and long dsRNAs havingsubstantial sequence identity to all or a portion of SEQ ID NO: 1 or SEQID NO: 3 may be used to inhibit the expression of a nucleic acid of theinvention, and particularly when the polynucleotide is expressed in amammalian or plant cell.

The nucleic acids of the invention may be used as diagnostic reagents todetect the presence or absence of the target DNA or RNA sequences towhich they specifically bind, such as for determining the level ofexpression of a nucleic acid of the invention. In one aspect, thepresent invention contemplates a method for detecting the presence of anucleic acid of the invention or a portion thereof in a sample, themethod comprising: (a) providing an oligonucleotide at least eightnucleotides in length, the oligonucleotide being complementary to aportion of a nucleic acid of the invention; (b) contacting theoligonucleotide with a sample comprising at least one nucleic acid underconditions that permit hybridization of the oligonucleotide with anucleic acid comprising a nucleotide sequence complementary thereto; and(c) detecting hybridization of the oligonucleotide to a nucleic acid inthe sample, thereby detecting the presence of a nucleic acid of theinvention or a portion thereof in the sample. In another aspect, thepresent invention contemplates a method for detecting the presence of anucleic acid of the invention or a portion thereof in a sample, themethod comprising: (a) providing a pair of single strandedoligonucleotides, each of which is at least eight nucleotides in length,complementary to sequences of a nucleic acid of the invention, andwherein the sequences to which the oligonucleotides are complementaryare at least ten nucleotides apart; and (b) contacting theoligonucleotides with a sample comprising at least one nucleic acidunder hybridization conditions; (c) amplifying the nucleotide sequencebetween the two oligonucleotide primers; and (d) detecting the presenceof the amplified sequence, thereby detecting the presence of a nucleicacid comprising the nucleic acid of the invention or a portion thereofin the sample.

In another aspect of the invention, the subject nucleic acid is providedin an expression vector comprising a nucleotide sequence encoding apolypeptide of the invention and operably linked to at least oneregulatory sequence. It should be understood that the design of theexpression vector may depend on such factors as the choice of the hostcell to be transformed and/or the type of protein desired to beexpressed. The vector's copy number, the ability to control that copynumber and the expression of any other protein encoded by the vector,such as antibiotic markers, should be considered.

The subject nucleic acids may be used to cause expression andover-expression of a polypeptide of the invention in cells propagated inculture, e.g. to produce proteins or polypeptides, including fusionproteins or polypeptides.

This invention pertains to a host cell transfected with a recombinantgene in order to express a polypeptide of the invention. The host cellmay be any prokaryotic or eukaryotic cell. For example, a polypeptide ofthe invention may be expressed in bacterial cells, such as E. coli,insect cells (baculovirus), yeast, or mammalian cells. In thoseinstances when the host cell is human, it may or may not be in a livesubject. Other suitable host cells are known to those skilled in theart. Additionally, the host cell may be supplemented with tRNA moleculesnot typically found in the host so as to optimize expression of thepolypeptide. Other methods suitable for maximizing expression of thepolypeptide will be known to those in the art.

The present invention further pertains to methods of producing thepolypeptides of the invention. For example, a host cell transfected withan expression vector encoding a polypeptide of the invention may becultured under appropriate conditions to allow expression of thepolypeptide to occur. The polypeptide may be secreted and isolated froma mixture of cells and medium containing the polypeptide. Alternatively,the polypeptide may be retained cytoplasmically and the cells harvested,lysed and the protein isolated.

A cell culture includes host cells, media and other byproducts. Suitablemedia for cell culture are well known in the art. The polypeptide may beisolated from cell culture medium, host cells, or both using techniquesknown in the art for purifying proteins, including ion-exchangechromatography, gel filtration chromatography, ultrafiltration,electrophoresis, and immunoaffinity purification with antibodiesspecific for particular epitopes of a polypeptide of the invention.

Thus, a nucleotide sequence encoding all or a selected portion ofpolypeptide of the invention, may be used to produce a recombinant formof the protein via microbial or eukaryotic cellular processes. Ligatingthe sequence into a polynucleotide construct, such as an expressionvector, and transforming or transfecting into hosts, either eukaryotic(yeast, avian, insect or mammalian) or prokaryotic (bacterial cells),are standard procedures. Similar procedures, or modifications thereof,may be employed to prepare recombinant polypeptides of the invention bymicrobial means or tissue-culture technology.

Expression vehicles for production of a recombinant protein includeplasmids and other vectors. For instance, suitable vectors for theexpression of a polypeptide of the invention include plasmids of thetypes: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derivedplasmids, pBTac-derived plasmids and pUC-derived plasmids for expressionin prokaryotic cells, such as E. coli.

A number of vectors exist for the expression of recombinant proteins inyeast. For instance, YEP24, YIP5, YEPS1, YEP52, pYES2, and YRP17 arecloning and expression vehicles useful in the introduction of geneticconstructs into S. cerevisiae (see, for example, Broach et al., (1983)in Experimental Manipulation of Gene Expression, ed. M. Inouye AcademicPress, p. 83). These vectors may replicate in E. coli due the presenceof the pBR322 ori, and in S. cerevisiae due to the replicationdeterminant of the yeast 2 micron plasmid. In addition, drug resistancemarkers such as ampicillin may be used.

In certain embodiments, mammalian expression vectors contain bothprokaryotic sequences to facilitate the propagation of the vector inbacteria, and one or more eukaryotic transcription units that areexpressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV,pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo andpHyg derived vectors are examples of mammalian expression vectorssuitable for transfection of eukaryotic cells. Some of these vectors aremodified with sequences from bacterial plasmids, such as pBR322, tofacilitate replication and drug resistance selection in both prokaryoticand eukaryotic cells. Alternatively, derivatives of viruses such as thebovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo,pREP-derived and p205) can be used for transient expression of proteinsin eukaryotic cells. The various methods employed in the preparation ofthe plasmids and transformation of host organisms are well known in theart. For other suitable expression systems for both prokaryotic andeukaryotic cells, as well as general recombinant procedures, seeMolecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritschand Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and17. In some instances, it may be desirable to express the recombinantprotein by the use of a baculovirus expression system. Examples of suchbaculovirus expression systems include pVL-derived vectors (such aspVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUWI),and pBlueBac-derived vectors (such as the β-gal containing pBlueBacIII).

In another variation, protein production may be achieved using in vitrotranslation systems. In vitro translation systems are, generally, atranslation system which is a cell-free extract containing at least theminimum elements necessary for translation of an RNA molecule into aprotein. An in vitro translation system typically comprises at leastribosomes, tRNAs, initiator methionyl-tRNAMet, proteins or complexesinvolved in translation, e.g., eIF2, eIF3, the cap-binding (CB) complex,comprising the cap-binding protein (CBP) and eukaryotic initiationfactor 4F (eIF4F). A variety of in vitro translation systems are wellknown in the art and include commercially available kits. Examples of invitro translation systems include eukaryotic lysates, such as rabbitreticulocyte lysates, rabbit oocyte lysates, human cell lysates, insectcell lysates and wheat germ extracts. Lysates are commercially availablefrom manufacturers such as Promega Corp., Madison, Wis.; Stratagene, LaJolla, Calif.; Amersham, Arlington Heights, Ill.; and GIBCO/BRL, GrandIsland, N.Y. In vitro translation systems typically comprisemacromolecules, such as enzymes, translation, initiation and elongationfactors, chemical reagents, and ribosomes. In addition, an in vitrotranscription system may be used. Such systems typically comprise atleast an RNA polymerase holoenzyme, ribonucleotides and any necessarytranscription initiation, elongation and termination factors. In vitrotranscription and translation may be coupled in a one-pot reaction toproduce proteins from one or more isolated DNAs.

When expression of a carboxy terminal fragment of a polypeptide isdesired, i.e. a truncation mutant, it may be necessary to add a startcodon (ATG) to the oligonucleotide fragment containing the desiredsequence to be expressed. It is well known in the art that a methionineat the N-terminal position may be enzymatically cleaved by the use ofthe enzyme methionine aminopeptidase (MAP). MAP has been cloned from E.coli (Ben-Bassat et al., (1987) J. Bacteriol. 169:751-757) andSalmonella typhimurium and its in vitro activity has been demonstratedon recombinant proteins (Miller et al., (1987) PNAS USA 84:2718-1722).Therefore, removal of an N-terminal methionine, if desired, may beachieved either in vivo by expressing such recombinant polypeptides in ahost which produces MAP (e.g., E. coli or CM89 or S. cerevisiae), or invitro by use of purified MAP (e.g., procedure of Miller et al.).

Coding sequences for a polypeptide of interest may be incorporated as apart of a fusion gene including a nucleotide sequence encoding adifferent polypeptide. The present invention contemplates an isolatednucleic acid comprising a nucleic acid of the invention and at least oneheterologous sequence encoding a heterologous peptide linked in frame tothe nucleotide sequence of the nucleic acid of the invention so as toencode a fusion protein comprising the heterologous polypeptide. Theheterologous polypeptide may be fused to (a) the C-terminus of thepolypeptide encoded by the nucleic acid of the invention, (b) theN-terminus of the polypeptide, or (c) the C-terminus and the N-terminusof the polypeptide. In certain instances, the heterologous sequenceencodes a polypeptide permitting the detection, isolation,solubilization and/or stabilization of the polypeptide to which it isfused. In still other embodiments, the heterologous sequence encodes apolypeptide selected from the group consisting of a polyHis tag, myc,HA, GST, protein A, protein G, calmodulin-binding peptide, thioredoxin,maltose-binding protein, poly arginine, poly His-Asp, FLAG, a portion ofan immunoglobulin protein, and a transcytosis peptide.

Fusion expression systems can be useful when it is desirable to producean immunogenic fragment of a polypeptide of the invention. For example,the VP6 capsid protein of rotavirus may be used as an immunologiccarrier protein for portions of polypeptide, either in the monomericform or in the form of a viral particle. The nucleic acid sequencescorresponding to the portion of a polypeptide of the invention to whichantibodies are to be raised may be incorporated into a fusion geneconstruct which includes coding sequences for a late vaccinia virusstructural protein to produce a set of recombinant viruses expressingfusion proteins comprising a portion of the protein as part of thevirion. The Hepatitis B surface antigen may also be utilized in thisrole as well. Similarly, chimeric constructs coding for fusion proteinscontaining a portion of a polypeptide of the invention and thepoliovirus capsid protein may be created to enhance immunogenicity (see,for example, EP Publication NO: 0259149; and Evans et al., (1989) Nature339:385; Huang et al., (1988) J. Virol. 62:3855; and Schlienger et al.,(1992) J. Virol. 66:2).

Fusion proteins may facilitate the expression and/or purification ofproteins. For example, a polypeptide of the invention may be generatedas a glutathione-S-transferase (GST) fusion protein. Such GST fusionproteins may be used to simplify purification of a polypeptide of theinvention, such as through the use of glutathione-derivatized matrices(see, for example, Current Protocols in Molecular Biology, eds. Ausubelet al., (N.Y.: John Wiley & Sons, 1991)). In another embodiment, afusion gene coding for a purification leader sequence, such as apoly-(His)/enterokinase cleavage site sequence at the N-terminus of thedesired portion of the recombinant protein, may allow purification ofthe expressed fusion protein by affinity chromatography using a Ni²⁺metal resin. The purification leader sequence may then be subsequentlyremoved by treatment with enterokinase to provide the purified protein(e.g., see Hochuli et al., (1987) J. Chromatography 411: 177; andJanknecht et al., PNAS USA 88:8972).

Techniques for making fusion genes are well known. Essentially, thejoining of various DNA fragments coding for different polypeptidesequences is performed in accordance with conventional techniques,employing blunt-ended or stagger-ended termini for ligation, restrictionenzyme digestion to provide for appropriate termini, filling-in ofcohesive ends as appropriate, alkaline phosphatase treatment to avoidundesirable joining, and enzymatic ligation. In another embodiment, thefusion gene may be synthesized by conventional techniques includingautomated DNA synthesizers. Alternatively, PCR amplification of genefragments may be carried out using anchor primers which give rise tocomplementary overhangs between two consecutive gene fragments which maysubsequently be annealed to generate a chimeric gene sequence (see, forexample, Current Protocols in Molecular Biology, eds. Ausubel et al.,John Wiley & Sons: 1992).

The present invention further contemplates a transgenic non-human animalhaving cells which harbor a transgene comprising a nucleic acid of theinvention.

In other embodiments, the invention provides for nucleic acids of theinvention immobilized onto a solid surface, including, plates,microtiter plates, slides, beads, particles, spheres, films, strands,precipitates, gels, sheets, tubing, containers, capillaries, pads,slices, etc. The nucleic acids of the invention may be immobilized ontoa chip as part of an array. The array may comprise one or morepolynucleotides of the invention as described herein. In one embodiment,the chip comprises one or more polynucleotides of the invention as partof an array of E. faecalis polynucleotide sequences.

In still other embodiments, the invention comprises the sequence of anucleic acid of the invention in computer readable format. The inventionalso encompasses a database comprising the sequence of a nucleic acid ofthe invention.

4. Homology Searching of Nucleotide and Polypeptide Sequences

The nucleotide or amino acid sequences of the invention, including thoseset forth in the appended Figures, may be used as query sequencesagainst databases such as GenBank, SwissProt, PDB, BLOCKS, and Pima II.These databases contain previously identified and annotated sequencesthat may be searched for regions of homology (similarity) using BLAST,which stands for Basic Local Alignment Search Tool (Altschul S F (1993)J Mol Evol 36:290-300; Altschul, S F et al (1990) J Mol Biol215:403-10).

BLAST produces alignments of both nucleotide and amino acid sequences todetermine sequence similarity. Because of the local nature of thealignments, BLAST is especially useful in determining exact matches orin identifying homologs which may be of prokaryotic (bacterial) oreukaryotic (animal, fungal or plant) origin. Other algorithms such asthe one described in Smith, R. F. and T. F. Smith (1992; ProteinEngineering 5:35-51) may be used when dealing with primary sequencepatterns and secondary structure gap penalties. In the usual courseusing BLAST, sequences have lengths of at least 49 nucleotides and nomore than 12% uncalled bases (where N is recorded rather than A, C, G,or T).

The BLAST approach, as detailed in Karlin and Altschul (1993; Proc NatAcad Sci 90:5873-7) searches matches between a query sequence and adatabase sequence, to evaluate the statistical significance of anymatches found, and to report only those matches which satisfy theuser-selected threshold of significance. The threshold is typically setat about 10-25 for nucleotides and about 3-15 for peptides.

5. Analysis of Protein Properties

(a) Analysis of Proteins by Mass Spectrometry

Typically, protein characterization by mass spectroscopy first requiresprotein isolation followed by either chemical or enzymatic digestion ofthe protein into smaller peptide fragments, whereupon the peptidefragments may be analyzed by mass spectrometry to obtain a peptide map.Mass spectrometry may also be used to identify post-translationalmodifications (e.g., phosphorylation, etc.) of a polypeptide.

Various mass spectrometers may be used within the present invention.Representative examples include: triple quadrupole mass spectrometers,magnetic sector instruments (magnetic tandem mass spectrometer, JEOL,Peabody, Mass.), ionspray mass spectrometers (Bruins et al., Anal Chem.59:2642-2647, 1987), electrospray mass spectrometers (including tandem,nano- and nano-electrospray tandem) (Fenn et al., Science 246:64-71,1989), laser desorption time-of-flight mass spectrometers (Karas andHillenkamp, Anal. Chem. 60:2299-2301, 1988), and a Fourier Transform IonCyclotron Resonance Mass Spectrometer (Extrel Corp., Pittsburgh, Mass.).

MALDI ionization is a technique in which samples of interest, in thiscase peptides and proteins, are co-crystallized with an acidifiedmatrix. The matrix is typically a small molecule that absorbs at aspecific wavelength, generally in the ultraviolet (UV) range, anddissipates the absorbed energy thermally. Typically a pulsed laser beamis used to transfer energy rapidly (i.e., a few ns) to the matrix. Thistransfer of energy causes the matrix to rapidly dissociate from theMALDI plate surface and results in a plume of matrix and theco-crystallized analytes being transferred into the gas phase. MALDI isconsidered a “soft-ionization” method that typically results insingly-charged species in the gas phase, most often resulting from aprotonation reaction with the matrix. MALDI may be coupled in-line withtime of flight (TOF) mass spectrometers. TOF detectors are based on theprinciple that an analyte moves with a velocity proportional to itsmass. Analytes of higher mass move slower than analytes of lower massand thus reach the detector later than lighter analytes. The presentinvention contemplates a composition comprising a polypeptide of theinvention and a matrix suitable for mass spectrometry. In certaininstances, the matrix is a nicotinic acid derivative or a cinnamic acidderivative.

MALDI-TOF MS is easily performed with modern mass spectrometers.Typically the samples of interest, in this case peptides or proteins,are mixed with a matrix and spotted onto a polished stainless steelplate (MALDI plate). Commercially available MALDI plates can presentlyhold up to 1536 samples per plate. Once spotted with sample, the MALDIsample plate is then introduced into the vacuum chamber of a MALDI massspectrometer. The pulsed laser is then activated and the mass to chargeratios of the analytes are measured utilizing a time of flight detector.A mass spectrum representing the mass to charge ratios of thepeptides/proteins is generated.

As mentioned above, MALDI can be utilized to measure the mass to chargeratios of both proteins and peptides. In the case of proteins, a mixtureof intact protein and matrix are co-crystallized on a MALDI target(Karas, M. and Hillenkamp, F. Anal. Chem. 1988, 60 (20) 2299-2301). Thespectrum resulting from this analysis is employed to determine themolecular weight of a whole protein. This molecular weight can then becompared to the theoretical weight of the protein and utilized incharacterizing the analyte of interest, such as whether or not theprotein has undergone post-translational modifications (e.g., examplephosphorylation).

In certain embodiments, MALDI mass spectrometry is used fordetermination of peptide maps of digested proteins. The peptide massesare measured accurately using a MALDI-TOF or a MALDI-Q-Star massspectrometer, with detection precision down to the low ppm (parts permillion) level. The ensemble of the peptide masses observed in a proteindigest, such as a tryptic digest, may be used to search protein/DNAdatabases in a method called peptide mass fingerprinting. In thisapproach, protein entries in a database are ranked according to thenumber of experimental peptide masses that match the predicted trypsindigestion pattern. Commercially available software utilizes a searchalgorithm that provides a scoring scheme based on the size of thedatabases, the number of matching peptides, and the different peptides.Depending on the number of peptides observed, the accuracy of themeasurement, and the size of the genome of the particular species,unambiguous protein identification may be obtained.

Statistical analysis may be performed upon each protein match todetermine the validity of the match. Typical constraints include errortolerances within 0.1 Da for monoisotopic peptide masses, cysteines maybe alkylated and searched as carboxyamidomethyl modifications, 0 or 1missed enzyme cleavages, and no methionine oxidations allowed.Identified proteins may be stored automatically in a relational databasewith software links to SDS-PAGE images and ligand sequences. Often evena partial peptide map is specific enough for identification of theprotein. If no protein match is found, a more error-tolerant search canbe used, for example using fewer peptides or allowing a larger marginerror with respect to mass accuracy.

Other mass spectroscopy methods such as tandem mass spectrometry or postsource decay may be used to obtain sequence information about proteinsthat cannot be identified by peptide mass mapping, or to confirm theidentity of proteins that are tentatively identified by anerror-tolerant peptide mass search described above. (Griffin et al,Rapid Commun. Mass. Spectrom. 1995, 9, 1546-51).

(b) Analysis of Proteins by Nuclear Magnetic Resonance (NMR)

NMR may be used to characterize the structure of a polypeptide inaccordance with the methods of the invention. In particular, NMR can beused, for example, to determine the three dimensional structure, theconformational state, the aggregation level, the state of proteinfolding/unfolding or the dynamic properties of a polypeptide. Forexample, the present invention contemplates a method for determiningthree dimensional structure information of a polypeptide of theinvention, the method comprising: (a) generating a purified isotopicallylabeled polypeptide of the invention; and (b) subjecting the polypeptideto NMR spectroscopic analysis, thereby determining information about itsthree dimensional structure.

Interaction between a polypeptide and another molecule can also bemonitored using NMR. Thus, the invention encompasses methods fordetecting, designing and characterizing interactions between apolypeptide and another molecule, including polypeptides, nucleic acidsand small molecules, utilizing NMR techniques. For example, the presentinvention contemplates a method for determining three dimensionalstructure information of a polypeptide of the invention, or a fragmentthereof, while the polypeptide is complexed with another molecule, themethod comprising: (a) generating a purified isotopically labeledpolypeptide of the invention, or a fragment thereof; (b) forming acomplex between the polypeptide and the other molecule; and (c)subjecting the complex to NMR spectroscopic analysis, therebydetermining information about the three dimensional structure of thepolypeptide. In another aspect, the present invention contemplates amethod for identifying compounds that bind to a polypeptide of theinvention, or a fragment thereof, the method comprising: (a) generatinga first NMR spectrum of an isotopically labeled polypeptide of theinvention, or a fragment thereof; (b) exposing the polypeptide to one ormore chemical compounds; (c) generating a second NMR spectrum of thepolypeptide which has been exposed to one or more chemical compounds;and (d) comparing the first and second spectra to determine differencesbetween the first and the second spectra, wherein the differences areindicative of one or more compounds that have bound to the polypeptide.

Briefly, the NMR technique involves placing the material to be examined(usually in a suitable solvent) in a powerful magnetic field andirradiating it with radio frequency (rf) electromagnetic radiation. Thenuclei of the various atoms will align themselves with the magneticfield until energized by the rf radiation. They then absorb thisresonant energy and re-radiate it at a frequency dependent on i) thetype of nucleus and ii) its atomic environment. Moreover, resonantenergy may be passed from one nucleus to another, either through bondsor through three-dimensional space, thus giving information about theenvironment of a particular nucleus and nuclei in its vicinity.

However, it is important to recognize that not all nuclei are NMRactive. Indeed, not all isotopes of the same element are active. Forexample, whereas “ordinary” hydrogen,

¹H, is NMR active, heavy hydrogen (deuterium), ²H, is not active in thesame way. Thus, any material that normally contains ¹H hydrogen may berendered “invisible” in the hydrogen NMR spectrum by replacing all oralmost all the ¹H hydrogens with 2H. It is for this reason that NMRspectroscopic analyses of water-soluble materials frequently areperformed in ²H₂O (or deuterium) to eliminate the water signal.

Conversely, “ordinary” carbon, ¹²C, is NMR inactive whereas the stableisotope,

¹³C, present to about 1% of total carbon in nature, is active.Similarly, while “ordinary” nitrogen, 14N, is NMR active, it hasundesirable properties for NMR and resonates at a different frequencyfrom the stable isotope ¹⁵N, present to about 0.4% of total nitrogen innature.

By labeling proteins with ¹⁵N and ¹⁵N/¹³C, it is possible to conductanalytical NMR of macromolecules with weights of 15 kD and 40 kD,respectively. More recently, partial deuteration of the protein inaddition to ¹³C- and ¹⁵N-labeling has increased the possible weight ofproteins and protein complexes for NMR analysis still further, toapproximately 60-70 kD. See Shan et al., J. Am. Chem. Soc.,118:6570-6579 (1996); L. E. Kay, Methods Enzymol., 339:174-203 (2001);and K. H. Gardner & L. E. Kay, Annu Rev Biophys Biomol Struct.,27:357-406 (1998); and references cited therein.

Isotopic substitution may be accomplished by growing a bacterium oryeast or other type of cultured cells, transformed by geneticengineering to produce the protein of choice, in a growth mediumcontaining ¹³C-, ¹⁵N- and/or ²H-labeled substrates. In certaininstances, bacterial growth media consists of ¹³C-labeled glucose and/or¹⁵N-labeled ammonium salts dissolved in D₂O where necessary. Kay, L. etal., Science, 249:411 (1990) and references therein and Bax, A., J. Am.Chem. Soc., 115, 4369 (1993). More recently, isotopically labeled mediaespecially adapted for the labeling of bacterially producedmacromolecules have been described. See U.S. Pat. No. 5,324,658.

The goal of these methods has been to achieve universal and/or randomisotopic enrichment of all of the amino acids of the protein. Bycontrast, other methods allow only certain residues to be relativelyenriched in ¹H, ²H, ¹³C and ¹⁵N. For example, Kay et al., J. Mol. Biol.,263, 627-636 (1996) and Kay et al., J. Am. Chem. Soc., 119, 7599-7600(1997) have described methods whereby isoleucine, alanine, valine andleucine residues in a protein may be labeled with ²H, ¹³C and ¹⁵N, andmay be specifically labeled with ¹H at the terminal methyl position. Inthis way, study of the proton-proton interactions between some aminoacids may be facilitated. Similarly, a cell-free system has beendescribed by Yokoyama et al., J. Biomol. NMR, 6(2), 129-134 (1995),wherein a transcription-translation system derived from E. coli was usedto express human Ha-Ras protein incorporating ¹⁵N into serine and/oraspartic acid.

Techniques for producing isotopically labeled proteins andmacromolecules, such as glycoproteins, in mammalian or insect cells havebeen described. See U.S. Pat. Nos. 5,393,669 and 5,627,044; Weller, C.T., Biochem., 35, 8815-23 (1996) and Lustbader, J. W., J. Biomol. NMR,7, 295-304 (1996). Other methods for producing polypeptides and othermolecules with labels appropriate for NMR are known in the art.

The present invention contemplates using a variety of solvents which areappropriate for NMR. For ¹H NMR, a deuterium lock solvent may be used.Exemplary deuterium lock solvents include acetone (CD₃COCD₃), chloroform(CDCl₃), dichloro methane (CD₂Cl₂), methylnitrile (CD₃CN), benzene(C₆D₆), water (D₂O), diethylether ((CD₃CD₂)₂O), dimethylether ((CD₃)₂O),N,N-dimethylformamide ((CD₃)₂NCDO), dimethyl sulfoxide (CD₃SOCD₃),ethanol (CD₃CD₂OD), methanol (CD₃OD), tetrahydrofuran (C₄D₈O), toluene(C₆D₅CD₃), pyridine (C₅D₅N) and cyclohexane (C₆H₁₂). For example, thepresent invention contemplates a composition comprising a polypeptide ofthe invention and a deuterium lock solvent.

The 2-dimensional ¹H-¹⁵N HSQC (Heteronuclear Single Quantum Correlation)spectrum provides a diagnostic fingerprint of conformational state,aggregation level, state of protein folding, and dynamic properties of apolypeptide (Yee et al, PNAS 99, 1825-30 (2002)). Polypeptides inaqueous solution usually populate an ensemble of 3-dimensionalstructures which can be determined by NMR. When the polypeptide is astable globular protein or domain of a protein, then the ensemble ofsolution structures is one of very closely related conformations. Inthis case, one peak is expected for each non-proline residue with adispersion of resonance frequencies with roughly equal intensity.Additional pairs of peaks from side-chain NH₂ groups are also oftenobserved, and correspond to the approximate number of Gln and Asnresidues in the protein. This type of HSQC spectra usually indicatesthat the protein is amenable to structure determination by NMR methods.

If the HSQC spectrum shows well-dispersed peaks but there are either toofew or too many in number, and/or the peak intensities differ throughoutthe spectrum, then the protein likely does not exist in a singleglobular conformation. Such spectral features are indicative ofconformational heterogeneity with slow or nonexistent inter-conversionbetween states (too many peaks) or the presence of dynamic processes onan intermediate timescale that can broaden and obscure the NMR signals.Proteins with this type of spectrum can sometimes be stabilized into asingle conformation by changing either the protein construct, thesolution conditions, temperature or by binding of another molecule.

The ¹H-¹⁵N HSQC can also indicate whether a protein has formed largenonspecific aggregates or has dynamic properties. Alternatively,proteins that are largely unfolded, e.g., having very little regularsecondary structure, result in ¹H-¹⁵N HSQC spectra in which the peaksare all very narrow and intense, but have very little spectraldispersion in the ¹⁵N-dimension. This reflects the fact that many ormost of the amide groups of amino acids in unfolded polypeptides aresolvent exposed and experience similar chemical environments resultingin similar ¹H chemical shifts.

The use of the ¹H-¹⁵N HSQC, can thus allow the rapid characterization ofthe conformational state, aggregation level, state of protein folding,and dynamic properties of a polypeptide. Additionally, other 2D spectrasuch as ¹H-¹³C HSQC, or HNCO spectra can also be used in a similarmanner. Further use of the ¹H-¹⁵N HSQC combined with relaxationmeasurements can reveal the molecular rotational correlation time anddynamic properties of polypeptides. The rotational correlation time isproportional to size of the protein and therefore can reveal if it formsspecific homo-oligomers such as homodimers, homotetramers, etc.

The structure of stable globular proteins can be determined through aseries of well-described procedures. For a general review of structuredetermination of globular proteins in solution by NMR spectroscopy, seeWüthrich, Science 243: 45-50 (1989). See also, Billeter et al., J. Mol.Biol. 155: 321-346 (1982). Current methods for structure determinationusually require the complete or nearly complete sequence-specificassignment of ¹H-resonance frequencies of the protein and subsequentidentification of approximate inter-hydrogen distances (from nuclearOverhauser effect (NOE) spectra) for use in restrained moleculardynamics calculations of the protein conformation. One approach for theanalysis of NMR resonance assignments was first outlined by Wüthrich,Wagner and co-workers (Wüthrich, “NMR or proteins and nucleic acids”Wiley, New York, N.Y. (1986); Wüthrich, Science 243: 45-50 (1989);Billeter et al., J. Mol. Biol. 155: 321-346 (1982)). Newer methods fordetermining the structures of globular proteins include the use ofresidual dipolar coupling restraints (Tian et al., J Am Chem Soc. 2001Nov. 28; 123(47):11791-6; Bax et al, Methods Enzymol. 2001; 339:127-74)and empirically derived conformational restraints (Zweckstetter & Bax, JAm Chem Soc. 2001 Sep. 26; 123(38):9490-1). It has also been shown thatit may be possible to determine structures of globular proteins usingonly un-assigned NOE measurements. NMR may also be used to determineensembles of many inter-converting, unfolded conformations (Choy andForman-Kay, J Mol. Biol. 2001 May 18; 308(5):1011-32).

NMR analysis of a polypeptide in the presence and absence of a testcompound (e.g., a polypeptide, nucleic acid or small molecule) may beused to characterize interactions between a polypeptide and anothermolecule. Because the ¹H-¹⁵N HSQC spectrum and other simple 2D NMRexperiments can be obtained very quickly (on the order of minutesdepending on protein concentration and NMR instrumentation), they arevery useful for rapidly testing whether a polypeptide is able to bind toanother molecule. Changes in the resonance frequency (in one or bothdimensions) of one or more peaks in the HSQC spectrum indicate aninteraction with another molecule. Often only a subset of the peaks willhave changes in resonance frequency upon binding to anther molecule,allowing one to map onto the structure those residues directly involvedin the interaction or involved in conformational changes as a result ofthe interaction. If the interacting molecule is relatively large(protein or nucleic acid) the peak widths will also broaden due to theincreased rotational correlation time of the complex. In some cases thepeaks involved in the interaction may actually disappear from the NMRspectrum if the interacting molecule is in intermediate exchange on theNMR timescale (i.e., exchanging on and off the polypeptide at afrequency that is similar to the resonance frequency of the monitorednuclei).

To facilitate the acquisition of NMR data on a large number of compounds(e.g., a library of synthetic or naturally-occurring small organiccompounds), a sample changer may be employed. Using the sample changer,a larger number of samples, numbering 60 or more, may be run unattended.To facilitate processing of the NMR data, computer programs are used totransfer and automatically process the multiple one-dimensional NMRdata.

In one embodiment, the invention provides a screening method foridentifying small molecules capable of interacting with a polypeptide ofthe invention. In one example, the screening process begins with thegeneration or acquisition of either a T₂-filtered or adiffusion-filtered one-dimensional proton spectrum of the compound ormixture of compounds. Means for generating T₂-filtered ordiffusion-filtered one-dimensional proton spectra are well known in theart (see, e.g., S. Meiboom and D. Gill, Rev. Sci. Instrum. 29:688(1958),S. J. Gibbs and C. S. Johnson, Jr. J. Main. Reson. 93:395-402 (1991) andA. S. Altieri, et al. J. Am. Chem. Soc. 117: 7566-7567 (1995)).

Following acquisition of the first spectrum for the molecules, the ¹⁵N-or ¹³C-labeled polypeptide is exposed to one or more molecules. Wheremore than one test compound is to be tested simultaneously, it ispreferred to use a library of compounds such as a plurality of smallmolecules. Such molecules are typically dissolved in perdeuterateddimethylsulfoxide. The compounds in the library may be purchased fromvendors or created according to desired needs.

Individual compounds may be selected inter alia on the basis of size andmolecular diversity for maximizing the possibility of discoveringcompounds that interact with widely diverse binding sites of apolypeptide of the invention.

The NMR screening process of the present invention utilizes a range oftest compound concentrations, e.g., from about 0.05 to about 1.0 mM. Atthose exemplary concentrations, compounds which are acidic or basic maysignificantly change the pH of buffered protein solutions. Chemicalshifts are sensitive to pH changes as well as direct bindinginteractions, and false-positive chemical shift changes, which are notthe result of test compound binding but of changes in pH, may thereforebe observed. It may therefore be necessary to ensure that the pH of thebuffered solution does not change upon addition of the test compound.

Following exposure of the test compounds to a polypeptide (e.g., thetarget molecule for the experiment) a second one-dimensional T₂- ordiffusion-filtered spectrum is generated. For the T₂-filtered approach,that second spectrum is generated in the same manner as set forth above.The first and second spectra are then compared to determine whetherthere are any differences between the two spectra. Differences in theone-dimensional T₂-filtered spectra indicate that the compound isbinding to, or otherwise interacting with, the target molecule. Thosedifferences are determined using standard procedures well known in theart. For the diffusion-filtered method, the second spectrum is generatedby looking at the spectral differences between low and high gradientstrengths—thus selecting for those compounds whose diffusion rates arecomparable to that observed in the absence of target molecule.

To discover additional molecules that bind to the protein, molecules areselected for testing based on the structure/activity relationships fromthe initial screen and/or structural information on the initial leadswhen bound to the protein. By way of example, the initial screening mayresult in the identification of compounds, all of which contain anaromatic ring. The second round of screening would then use otheraromatic molecules as the test compounds.

In another embodiment, the methods of the invention utilize a processfor detecting the binding of one ligand to a polypeptide in the presenceof a second ligand. In accordance with this embodiment, a polypeptide isbound to the second ligand before exposing the polypeptide to the testcompounds.

For more information on NMR methods encompassed by the presentinvention, see also: U.S. Pat. Nos. 5,668,734; 6,194,179; 6,162,627;6,043,024; 5,817,474; 5,891,642; 5,989,827; 5,891,643; 6,077,682; WO00/05414; WO 99/22019; Cavanagh, et al., Protein NMR Spectroscopy,Principles and Practice, 1996, Academic Press; Clore, et al., NMR ofProteins. In Topics in Molecular and Structural Biology, 1993, S.Neidle, Fuller, W., and Cohen, J. S., eds., Macmillan Press, Ltd.,London; and Christendat et al., Nature Structural Biology 7: 903-909(2000).

(c) Analysis of Proteins by X-ray Crystallography

(i) X-ray Structure Determination

Exemplary methods for obtaining the three dimensional structure of thecrystalline form of a molecule or complex are described herein and, inview of this specification, variations on these methods will be apparentto those skilled in the art (see Ducruix and Geige 1992, IRL Press,Oxford, England).

A variety of methods involving x-ray crystallography are contemplated bythe present invention. For example, the present invention contemplatesproducing a crystallized polypeptide of the invention, or a fragmentthereof, by: (a) introducing into a host cell an expression vectorcomprising a nucleic acid encoding for a polypeptide of the invention,or a fragment thereof; (b) culturing the host cell in a cell culturemedium to express the polypeptide or fragment; (c) isolating thepolypeptide or fragment from the cell culture; and (d) crystallizing thepolypeptide or fragment thereof. Alternatively, the present inventioncontemplates determining the three dimensional structure of acrystallized polypeptide of the invention, or a fragment thereof, by:(a) crystallizing a polypeptide of the invention, or a fragment thereof,such that the crystals will diffract x-rays to a resolution of 3.5 Å orbetter; and (b) analyzing the polypeptide or fragment by x-raydiffraction to determine the three-dimensional structure of thecrystallized polypeptide.

X-ray crystallography techniques generally require that the proteinmolecules be available in the form of a crystal. Crystals may be grownfrom a solution containing a purified polypeptide of the invention, or afragment thereof (e.g., a stable domain), by a variety of conventionalprocesses. These processes include, for example, batch, liquid, bridge,dialysis, vapour diffusion (e.g., hanging drop or sitting drop methods).(See for example, McPherson, 1982 John Wiley, New York; McPherson, 1990,Eur. J. Biochem. 189: 1-23; Webber. 1991, Adv. Protein Chem. 41:1-36).

In certain embodiments, native crystals of the invention may be grown byadding precipitants to the concentrated solution of the polypeptide. Theprecipitants are added at a concentration just below that necessary toprecipitate the protein. Water may be removed by controlled evaporationto produce precipitating conditions, which are maintained until crystalgrowth ceases.

The formation of crystals is dependent on a number of differentparameters, including pH, temperature, protein concentration, the natureof the solvent and precipitant, as well as the presence of added ions orligands to the protein. In addition, the sequence of the polypeptidebeing crystallized will have a significant affect on the success ofobtaining crystals. Many routine crystallization experiments may beneeded to screen all these parameters for the few combinations thatmight give crystal suitable for x-ray diffraction analysis (See, forexample, Jancarik, J & Kim, S. H., J. Appl. Cryst. 1991 24: 409-411).

Crystallization robots may automate and speed up the work ofreproducibly setting up large number of crystallization experiments.Once some suitable set of conditions for growing the crystal are found,variations of the condition may be systematically screened in order tofind the set of conditions which allows the growth of sufficientlylarge, single, well ordered crystals. In certain instances, apolypeptide of the invention is co-crystallized with a compound thatstabilizes the polypeptide.

A number of methods are available to produce suitable radiation forx-ray diffraction. For example, x-ray beams may be produced bysynchrotron rings where electrons (or positrons) are accelerated throughan electromagnetic field while traveling at close to the speed of light.Because the admitted wavelength may also be controlled, synchrotrons maybe used as a tunable x-ray source (Hendrickson W A., Trends Biochem Sci2000 December; 25(12):637-43). For less conventional Laue diffractionstudies, polychromatic x-rays covering a broad wavelength window areused to observe many diffraction intensities simultaneously (Stoddard,B. L., Curr. Opin. Struct Biol 1998 October; 8(5):612-8). Neutrons mayalso be used for solving protein crystal structures (Gutberlet T,Heinemann U & Steiner M., Acta Crystallogr D 2001; 57: 349-54).

Before data collection commences, a protein crystal may be frozen toprotect it from radiation damage. A number of different cryo-protectantsmay be used to assist in freezing the crystal, such as methylpentanediol (MPD), isopropanol, ethylene glycol, glycerol, formate,citrate, mineral oil, or a low-molecular-weight polyethylene glycol(PEG). The present invention contemplates a composition comprising apolypeptide of the invention and a cryo-protectant. As an alternative tofreezing the crystal, the crystal may also be used for diffractionexperiments performed at temperatures above the freezing point of thesolution. In these instances, the crystal may be protected from dryingout by placing it in a narrow capillary of a suitable material(generally glass or quartz) with some of the crystal growth solutionincluded in order to maintain vapour pressure.

X-ray diffraction results may be recorded by a number of ways know toone of skill in the art. Examples of area electronic detectors includecharge coupled device detectors, multi-wire area detectors andphosphoimager detectors (Amemiya, Y, 1997. Methods in Enzymology, Vol.276. Academic Press, San Diego, pp. 233-243; Westbrook, E. M., Naday, I.1997. Methods in Enzymology, Vol. 276. Academic Press, San Diego, pp.244-268; 1997. Kahn, R. & Fourme, R. Methods in Enzymology, Vol. 276.Academic Press, San Diego, pp. 268-286).

A suitable system for laboratory data collection might include a BrukerAXS Proteum R system, equipped with a copper rotating anode source,Confocal Max-Flux™ optics and a SMART 6000 charge coupled devicedetector. Collection of x-ray diffraction patterns are well documentedby those skilled in the art (See, for example, Ducruix and Geige, 1992,IRL Press, Oxford, England).

The theory behind diffraction by a crystal upon exposure to x-rays iswell known. Because phase information is not directly measured in thediffraction experiment, and is needed to reconstruct the electrondensity map, methods that can recover this missing information arerequired. One method of solving structures ab initio are thereal/reciprocal space cycling techniques. Suitable real/reciprocal spacecycling search programs include shake-and-bake (Weeks C M, DeTitta G T,Hauptman H A, Thuman P, Miller R Acta Crystallogr A 1994; V50: 210-20).

Other methods for deriving phases may also be needed. These techniquesgenerally rely on the idea that if two or more measurements of the samereflection are made where strong, measurable, differences areattributable to the characteristics of a small subset of the atomsalone, then the contributions of other atoms can be, to a firstapproximation, ignored, and positions of these atoms may be determinedfrom the difference in scattering by one of the above techniques.Knowing the position and scattering characteristics of those atoms, onemay calculate what phase the overall scattering must have had to producethe observed differences.

One version of this technique is isomorphous replacement technique,which requires the introduction of new, well ordered, x-ray scatterersinto the crystal. These additions are usually heavy metal atoms, (sothat they make a significant difference in the diffraction pattern); andif the additions do not change the structure of the molecule or of thecrystal cell, the resulting crystals should be isomorphous. Isomorphousreplacement experiments are usually performed by diffusing differentheavy-metal metals into the channels of a pre-existing protein crystal.Growing the crystal from protein that has been soaked in the heavy atomis also possible (Petsko, G. A., 1985. Methods in Enzymology, Vol. 114.Academic Press, Orlando, pp. 147-156). Alternatively, the heavy atom mayalso be reactive and attached covalently to exposed amino acid sidechains (such as the sulfur atom of cysteine) or it may be associatedthrough non-covalent interactions. It is sometimes possible to replaceendogenous light metals in metallo-proteins with heavier ones, e.g.,zinc by mercury, or calcium by samarium (Petsko, G. A., 1985. Methods inEnzymology, Vol. 114. Academic Press, Orlando, pp. 147-156). Exemplarysources for such heavy compounds include, without limitation, sodiumbromide, sodium selenate, trimethyl lead acetate, mercuric chloride,methyl mercury acetate, platinum tetracyanide, platinum tetrachloride,nickel chloride, and europium chloride.

A second technique for generating differences in scattering involves thephenomenon of anomalous scattering. X-rays that cause the displacementof an electron in an inner shell to a higher shell are subsequentlyrescattered, but there is a time lag that shows up as a phase delay.This phase delay is observed as a (generally quite small) difference inintensity between reflections known as Friedel mates that would beidentical if no anomalous scattering were present. A second effectrelated to this phenomenon is that differences in the intensity ofscattering of a given atom will vary in a wavelength dependent manner,given rise to what are known as dispersive differences. In principleanomalous scattering occurs with all atoms, but the effect is strongestin heavy atoms, and may be maximized by using x-rays at a wavelengthwhere the energy is equal to the difference in energy between shells.The technique therefore requires the incorporation of some heavy atommuch as is needed for isomorphous replacement, although for anomalousscattering a wider variety of atoms are suitable, including lightermetal atoms (copper, zinc, iron) in metallo-proteins. One method forpreparing a protein for anomalous scattering involves replacing themethionine residues in whole or in part with selenium containingseleno-methionine. Soaks with halide salts such as bromides and othernon-reactive ions may also be effective (Dauter Z, Li M, Wlodawer A.,Acta Crystallogr D 2001; 57: 239-49).

In another process, known as multiple anomalous scattering or MAD, twoto four suitable wavelengths of data are collected. (Hendrickson, W. A.and Ogata, C. M. 1997 Methods in Enzymology 276, 494-523). Phasing byvarious combinations of single and multiple isomorphous and anomalousscattering are possible too. For example, SIRAS (single isomorphousreplacement with anomalous scattering) utilizes both the isomorphous andanomalous differences for one derivative to derive phases. Moretraditionally, several different heavy atoms are soaked into differentcrystals to get sufficient phase information from isomorphousdifferences while ignoring anomalous scattering, in the technique knownas multiple isomorphous replacement (MIR) (Petsko, G. A., 1985. Methodsin Enzymology, Vol. 114. Academic Press, Orlando, pp. 147-156).

Additional restraints on the phases may be derived from densitymodification techniques. These techniques use either generally knownfeatures of electron density distribution or known facts about thatparticular crystal to improve the phases. For example, because proteinregions of the crystal scatter more strongly than solvent regions,solvent flattening/flipping may be used to adjust phases to make solventdensity a uniform flat value (Zhang, K. Y. J., Cowtan, K. and Main, P.Methods in Enzymology 277, 1997 Academic Press, Orlando pp 53-64). Ifmore than one molecule of the protein is present in the asymmetric unit,the fact that the different molecules should be virtually identical maybe exploited to further reduce phase error using non-crystallographicsymmetry averaging (Villieux, F. M. D. and Read, R. J. Methods inEnzymology 277, 1997 Academic Press, Orlando pp18-52). Suitable programsfor performing these processes include DM and other programs of the CCP4suite (Collaborative Computational Project, Number 4. 1994. Acta Cryst.D50, 760-763) and CNX.

The unit cell dimensions, symmetry, vector amplitude and derived phaseinformation can be used in a Fourier transform function to calculate theelectron density in the unit cell, i.e., to generate an experimentalelectron density map. This may be accomplished using programs of the CNXor CCP4 packages. The resolution is measured in Angstrom (A) units, andis closely related to how far apart two objects need to be before theycan be reliably distinguished. The smaller this number is, the higherthe resolution and therefore the greater the amount of detail that canbe seen. Preferably, crystals of the invention diffract x-rays to aresolution of better than about 4.0, 3.5, 3.0, 2.5, 2.0, 1.5, 1.0, 0.5 Åor better.

As used herein, the term “modeling” includes the quantitative andqualitative analysis of molecular structure and/or function based onatomic structural information and interaction models. The term“modeling” includes conventional numeric-based molecular dynamic andenergy minimization models, interactive computer graphic models,modified molecular mechanics models, distance geometry and otherstructure-based constraint models.

Model building may be accomplished by either the crystallographer usinga computer graphics program such as TURBO or 0 (Jones, T A. et al., ActaCrystallogr. A47, 100-119, 1991) or, under suitable circumstances, byusing a fully automated model building program, such as wARP (AnastassisPerrakis, Richard Morris & Victor S. Lamzin; Nature Structural Biology,May 1999 Volume 6 Number 5 pp 458-463) or MAID (Levitt, D. G., ActaCrystallogr. D 2001 V57: 1013-9). This structure may be used tocalculate model-derived diffraction amplitudes and phases. Themodel-derived and experimental diffraction amplitudes may be comparedand the agreement between them can be described by a parameter referredto as R-factor. A high degree of correlation in the amplitudescorresponds to a low R-factor value, with 0.0 representing exactagreement and 0.59 representing a completely random structure. Becausethe R-factor may be lowered by introducing more free parameters into themodel, an unbiased, cross-correlated version of the R-factor known asthe R-free gives a more objective measure of model quality. For thecalculation of this parameter a subset of reflections (generally around10%) are set aside at the beginning of the refinement and not used aspart of the refinement target. These reflections are then compared tothose predicted by the model (Kleywegt G J, Brunger A T, Structure 1996Aug. 15; 4(8):897-904).

The model may be improved using computer programs that maximize theprobability that the observed data was produced from the predictedmodel, while simultaneously optimizing the model geometry. For example,the CNX program may be used for model refinement, as can the XPLORprogram (1992, Nature 355:472-475, G. N. Murshudov, A. A. Vagin. and E.J. Dodson, (1997) Acta Cryst. D 53, 240-255). In order to maximize theconvergence radius of refinement, simulated annealing refinement usingtorsion angle dynamics may be employed in order to reduce the degrees offreedom of motion of the model (Adams P D, Pannu N S, Read R J, BrungerA T., Proc Natl Acad Sci U S A 1997 May 13; 94(10):5018-23). Whereexperimental phase information is available (e.g. where MAD data wascollected) Hendrickson-Lattman phase probability targets may beemployed. Isotropic or anisotropic domain, group or individualtemperature factor refinement, may be used to model variance of theatomic position from its mean. Well defined peaks of electron densitynot attributable to protein atoms are generally modeled as watermolecules. Water molecules may be found by manual inspection of electrondensity maps, or with automatic water picking routines. Additional smallmolecules, including ions, cofactors, buffer molecules or substrates maybe included in the model if sufficiently unambiguous electron density isobserved in a map.

In general, the R-free is rarely as low as 0.15 and may be as high as0.35 or greater for a reasonably well-determined protein structure. Theresidual difference is a consequence of approximations in the model(inadequate modeling of residual structure in the solvent, modelingatoms as isotropic Gaussian spheres, assuming all molecules areidentical rather than having a set of discrete conformers, etc.) anderrors in the data (Lattman E E., Proteins 1996; 25: i-ii). In refinedstructures at high resolution, there are usually no major errors in theorientation of individual residues, and the estimated errors in atomicpositions are usually around 0.1-0.2 up to 0.3 Å.

The three dimensional structure of a new crystal may be modeled usingmolecular replacement. The term “molecular replacement” refers to amethod that involves generating a preliminary model of a molecule orcomplex whose structure coordinates are unknown, by orienting andpositioning a molecule whose structure coordinates are known within theunit cell of the unknown crystal, so as best to account for the observeddiffraction pattern of the unknown crystal. Phases may then becalculated from this model and combined with the observed amplitudes togive an approximate Fourier synthesis of the structure whose coordinatesare unknown. This, in turn, can be subject to any of the several formsof refinement to provide a final, accurate structure of the unknowncrystal. Lattman, E., “Use of the Rotation and Translation Functions”,in Methods in Enzymology, 115, pp. 55-77 (1985); M. G. Rossmann, ed.,“The Molecular Replacement Method”, Int. Sci. Rev. Ser., No. 13, Gordon& Breach, New York, (1972).

Commonly used computer software packages for molecular replacement areCNX, X-PLOR (Brunger 1992, Nature 355: 472-475), AMoRE (Navaza, 1994,Acta Crystallogr. A50:157-163), the CCP4 package, the MERLOT package (P.M. D. Fitzgerald, J. Appl. Cryst., Vol. 21, pp. 273-278, 1988) andXTALVIEW (McCree et al (1992) J. Mol. Graphics 10: 44-46). The qualityof the model may be analyzed using a program such as PROCHECK or3D-Profiler (Laskowski et al 1993 J. Appl. Cryst. 26:283-291; Luthy R.et al, Nature 356: 83-85, 1992; and Bowie, J. U. et al, Science 253:164-170, 1991).

Homology modeling (also known as comparative modeling or knowledge-basedmodeling) methods may also be used to develop a three dimensional modelfrom a polypeptide sequence based on the structures of known proteins.The method utilizes a computer model of a known protein, a computerrepresentation of the amino acid sequence of the polypeptide with anunknown structure, and standard computer representations of thestructures of amino acids. This method is well known to those skilled inthe art (Greer, 1985, Science 228, 1055; Bundell et al 1988, Eur. J.Biochem. 172, 513; Knighton et al., 1992, Science 258:130-135,http://biochem.vt.edu/courses/-modeling/homology.htn). Computer programsthat can be used in homology modeling are QUANTA and the Homology modulein the Insight II modeling package distributed by Molecular SimulationsInc, or MODELLER (Rockefeller University,www.iucr.ac.uk/sinris-top/logical/prg-modeller.html).

Once a homology model has been generated it is analyzed to determine itscorrectness. A computer program available to assist in this analysis isthe Protein Health module in QUANTA which provides a variety of tests.Other programs that provide structure analysis along with output includePROCHECK and 3D-Profiler (Luthy R. et al, Nature 356: 83-85, 1992; andBowie, J. U. et al, Science 253: 164-170, 1991). Once any irregularitieshave been resolved, the entire structure may be further refined.

Other molecular modeling techniques may also be employed in accordancewith this invention. See, e.g., Cohen, N. C. et al, J. Med. Chem., 33,pp. 883-894 (1990). See also, Navix, M. A. and M. A. Marko, CurrentOpinions in Structural Biology, 2, pp. 202-210 (1992).

Under suitable circumstances, the entire process of solving a crystalstructure may be accomplished in an automated fashion by a system suchas ELVES$\frac{\left( {{{http}:}//{{{{ucxray}.{berkeley}.{edu}}\text{/}} \sim {{jamesh}\text{/}{elves}\text{/}{{index}.{html}}}}} \right)}{({ii})X\text{-}{ray}\quad{Structure}}$with little or no user intervention.

The present invention provides methods for determining some or all ofthe structural coordinates for amino acids of a polypeptide of theinvention, or a complex thereof.

In another aspect, the present invention provides methods foridentifying a druggable region of a polypeptide of the invention. Forexample, one such method includes: (a) obtaining crystals of apolypeptide of the invention or a fragment thereof such that the threedimensional structure of the crystallized protein can be determined to aresolution of 3.5 Å or better; (b) determining the three dimensionalstructure of the crystallized polypeptide or fragment using x-raydiffraction; and (c) identifying a druggable region of a polypeptide ofthe invention based on the three-dimensional structure of thepolypeptide or fragment.

A three dimensional structure of a molecule or complex may be describedby the set of atoms that best predict the observed diffraction data(that is, which possesses a minimal R value). Files may be created forthe structure that defines each atom by its chemical identity, spatialcoordinates in three dimensions, root mean squared deviation from themean observed position and fractional occupancy of the observedposition.

Those of skill in the art understand that a set of structure coordinatesfor an protein, complex or a portion thereof, is a relative set ofpoints that define a shape in three dimensions. Thus, it is possiblethat an entirely different set of coordinates could define a similar oridentical shape. Moreover, slight variations in the individualcoordinates may have little affect on overall shape. Such variations incoordinates may be generated because of mathematical manipulations ofthe structure coordinates. For example, structure coordinates could bemanipulated by crystallographic permutations of the structurecoordinates, fractionalization of the structure coordinates, integeradditions or subtractions to sets of the structure coordinates,inversion of the structure coordinates or any combination of the above.Alternatively, modifications in the crystal structure due to mutations,additions, substitutions, and/or deletions of amino acids, or otherchanges in any of the components that make up the crystal, could alsoyield variations in structure coordinates. Such slight variations in theindividual coordinates will have little affect on overall shape. If suchvariations are within an acceptable standard error as compared to theoriginal coordinates, the resulting three-dimensional shape isconsidered to be structurally equivalent. It should be noted that slightvariations in individual structure coordinates of a polypeptide of theinvention or a complex thereof would not be expected to significantlyalter the nature of modulators that could associate with a druggableregion thereof. Thus, for example, a modulator that bound to the activesite of a polypeptide of the invention would also be expected to bind toor interfere with another active site whose structure coordinates definea shape that falls within the acceptable error.

A crystal structure of the present invention may be used to make astructural or computer model of the polypeptide, complex or portionthereof. A model may represent the secondary, tertiary and/or quaternarystructure of the polypeptide, complex or portion. The configurations ofpoints in space derived from structure coordinates according to theinvention can be visualized as, for example, a holographic image, astereodiagram, a model or a computer-displayed image, and the inventionthus includes such images, diagrams or models.

(iii) Structural Equivalents

Various computational analyses can be used to determine whether amolecule or the active site portion thereof is structurally equivalentwith respect to its three-dimensional structure, to all or part of astructure of a polypeptide of the invention or a portion thereof.

For the purpose of this invention, any molecule or complex or portionthereof, that has a root mean square deviation of conserved residuebackbone atoms (N, Cα, C, O) of less than about 1.75 Å, whensuperimposed on the relevant backbone atoms described by the referencestructure coordinates of a polypeptide of the invention, is considered“structurally equivalent” to the reference molecule. That is to say, thecrystal structures of those portions of the two molecules aresubstantially identical, within acceptable error. Alternatively, theroot mean square deviation may be is less than about 1.50, 1.40, 1.25,1.0, 0.75, 0.5 or 0.35 Å.

The term “root mean square deviation” is understood in the art and meansthe square root of the arithmetic mean of the squares of the deviations.It is a way to express the deviation or variation from a trend orobject.

In another aspect, the present invention provides a scalablethree-dimensional configuration of points, at least a portion of saidpoints, and preferably all of said points, derived from structuralcoordinates of at least a portion of a polypeptide of the invention andhaving a root mean square deviation from the structure coordinates ofthe polypeptide of the invention of less than 1.50, 1.40, 1.25, 1.0,0.75, 0.5 or 0.35 Å. In certain embodiments, the portion of apolypeptide of the invention is 25%, 33%, 50%, 66%, 75%, 85%, 90% or 95%or more of the amino acid residues contained in the polypeptide.

In another aspect, the present invention provides a molecule or complexincluding a druggable region of a polypeptide of the invention, thedruggable region being defined by a set of points having a root meansquare deviation of less than about 1.75 Å from the structuralcoordinates for points representing (a) the backbone atoms of the aminoacids contained in a druggable region of a polypeptide of the invention,(b) the side chain atoms (and optionally the Cα atoms) of the aminoacids contained in such druggable region, or (c) all the atoms of theamino acids contained in such druggable region. In certain embodiments,only a portion of the amino acids of a druggable region may be includedin the set of points, such as 25%, 33%, 50%, 66%, 75%, 85%, 90% or 95%or more of the amino acid residues contained in the druggable region. Incertain embodiments, the root mean square deviation may be less than1.50, 1.40, 1.25, 1.0, 0.75, 0.5, or 0.35 Å. In still other embodiments,instead of a druggable region, a stable domain, fragment or structuralmotif is used in place of a druggable region.

(iv) Machine Displays and Machine Readable Storage Media

The invention provides a machine-readable storage medium including adata storage material encoded with machine readable data which, whenusing a machine programmed with instructions for using said data,displays a graphical three-dimensional representation of any of themolecules or complexes, or portions thereof, of this invention. Inanother embodiment, the graphical three-dimensional representation ofsuch molecule, complex or portion thereof includes the root mean squaredeviation of certain atoms of such molecule by a specified amount, suchas the backbone atoms by less than 0.8 Å. In another embodiment, astructural equivalent of such molecule, complex, or portion thereof, maybe displayed. In another embodiment, the portion may include a druggableregion of the polypeptide of the invention.

According to one embodiment, the invention provides a computer fordetermining at least a portion of the structure coordinatescorresponding to x-ray diffraction data obtained from a molecule orcomplex, wherein said computer includes: (a) a machine-readable datastorage medium comprising a data storage material encoded withmachine-readable data, wherein said data comprises at least a portion ofthe structural coordinates of a polypeptide of the invention; (b) amachine-readable data storage medium comprising a data storage materialencoded with machine-readable data, wherein said data comprises x-raydiffraction data from said molecule or complex; (c) a working memory forstoring instructions for processing said machine-readable data of (a)and (b); (d) a central-processing unit coupled to said working memoryand to said machine-readable data storage medium of (a) and (b) forperforming a Fourier transform of the machine readable data of (a) andfor processing said machine readable data of (b) into structurecoordinates; and (e) a display coupled to said central-processing unitfor displaying said structure coordinates of said molecule or complex.In certain embodiments, the structural coordinates displayed arestructurally equivalent to the structural coordinates of a polypeptideof the invention.

In an alternative embodiment, the machine-readable data storage mediumincludes a data storage material encoded with a first set of machinereadable data which includes the Fourier transform of the structurecoordinates of a polypeptide of the invention or a portion thereof, andwhich, when using a machine programmed with instructions for using saiddata, can be combined with a second set of machine readable dataincluding the x-ray diffraction pattern of a molecule or complex todetermine at least a portion of the structure coordinates correspondingto the second set of machine readable data.

For example, a system for reading a data storage medium may include acomputer including a central processing unit (“CPU”), a working memorywhich may be, e.g., RAM (random access memory) or “core” memory, massstorage memory (such as one or more disk drives or CD-ROM drives), oneor more display devices (e.g., cathode-ray tube (“CRT”) displays, lightemitting diode (“LED”) displays, liquid crystal displays (“LCDs”),electroluminescent displays, vacuum fluorescent displays, field emissiondisplays (“FEDs”), plasma displays, projection panels, etc.), one ormore user input devices (e.g., keyboards, microphones, mice, touchscreens, etc.), one or more input lines, and one or more output lines,all of which are interconnected by a conventional bidirectional systembus. The system may be a stand-alone computer, or may be networked(e.g., through local area networks, wide area networks, intranets,extranets, or the internet) to other systems (e.g., computers, hosts,servers, etc.). The system may also include additional computercontrolled devices such as consumer electronics and appliances.

Input hardware may be coupled to the computer by input lines and may beimplemented in a variety of ways. Machine-readable data of thisinvention may be inputted via the use of a modem or modems connected bya telephone line or dedicated data line. Alternatively or additionally,the input hardware may include CD-ROM drives or disk drives. Inconjunction with a display terminal, a keyboard may also be used as aninput device.

Output hardware may be coupled to the computer by output lines and maysimilarly be implemented by conventional devices. By way of example, theoutput hardware may include a display device for displaying a graphicalrepresentation of an active site of this invention using a program suchas QUANTA as described herein. Output hardware might also include aprinter, so that hard copy output may be produced, or a disk drive, tostore system output for later use.

In operation, a CPU coordinates the use of the various input and outputdevices, coordinates data accesses from mass storage devices, accessesto and from working memory, and determines the sequence of dataprocessing steps. A number of programs may be used to process themachine-readable data of this invention. Such programs are discussed inreference to the computational methods of drug discovery as describedherein. References to components of the hardware system are included asappropriate throughout the following description of the data storagemedium.

Machine-readable storage devices useful in the present inventioninclude, but are not limited to, magnetic devices, electrical devices,optical devices, and combinations thereof. Examples of such data storagedevices include, but are not limited to, hard disk devices, CD devices,digital video disk devices, floppy disk devices, removable hard diskdevices, magneto-optic disk devices, magnetic tape devices, flash memorydevices, bubble memory devices, holographic storage devices, and anyother mass storage peripheral device. It should be understood that thesestorage devices include necessary hardware (e.g., drives, controllers,power supplies, etc.) as well as any necessary media (e.g., disks, flashcards, etc.) to enable the storage of data.

In one embodiment, the present invention contemplates a computerreadable storage medium comprising structural data, wherein the datainclude the identity and three-dimensional coordinates of a polypeptideof the invention or portion thereof. In another aspect, the presentinvention contemplates a database comprising the identity andthree-dimensional coordinates of a polypeptide of the invention or aportion thereof. Alternatively, the present invention contemplates adatabase comprising a portion or all of the atomic coordinates of apolypeptide of the invention or portion thereof.

(v) Structurally Similar Molecules and Complexes

Structural coordinates for a polypeptide of the invention can be used toaid in obtaining structural information about another molecule orcomplex. This method of the invention allows determination of at least aportion of the three-dimensional structure of molecules or molecularcomplexes which contain one or more structural features that are similarto structural features of a polypeptide of the invention. Similarstructural features can include, for example, regions of amino acididentity, conserved active site or binding site motifs, and similarlyarranged secondary structural elements (e.g., a helices and β sheets).Many of the methods described above for determining the structure of apolypeptide of the invention may be used for this purpose as well.

For the present invention, a “structural homolog” is a polypeptide thatcontains one or more amino acid substitutions, deletions, additions, orrearrangements with respect to the amino acid sequence of SEQ ID NO: 4or other polypeptide of the invention, but that, when folded into itsnative conformation, exhibits or is reasonably expected to exhibit atleast a portion of the tertiary (three-dimensional) structure of thepolypeptide encoded by SEQ ID NO: 4 or such other polypeptide of theinvention. For example, structurally homologous molecules can containdeletions or additions of one or more contiguous or noncontiguous aminoacids, such as a loop or a domain. Structurally homologous moleculesalso include modified polypeptide molecules that have been chemically orenzymatically derivatized at one or more constituent amino acids,including side chain modifications, backbone modifications, and N- andC-terminal modifications including acetylation, hydroxylation,methylation, amidation, and the attachment of carbohydrate or lipidmoieties, cofactors, and the like.

By using molecular replacement, all or part of the structure coordinatesof a polypeptide of the invention can be used to determine the structureof a crystallized molecule or complex whose structure is unknown morequickly and efficiently than attempting to determine such information abinitio. For example, in one embodiment this invention provides a methodof utilizing molecular replacement to obtain structural informationabout a molecule or complex whose structure is unknown including: (a)crystallizing the molecule or complex of unknown structure; (b)generating an x-ray diffraction pattern from said crystallized moleculeor complex; and (c) applying at least a portion of the structurecoordinates for a polypeptide of the invention to the x-ray diffractionpattern to generate a three-dimensional electron density map of themolecule or complex whose structure is unknown.

In another aspect, the present invention provides a method forgenerating a preliminary model of a molecule or complex whose structurecoordinates are unknown, by orienting and positioning the relevantportion of a polypeptide of the invention within the unit cell of thecrystal of the unknown molecule or complex so as best to account for theobserved x-ray diffraction pattern of the crystal of the molecule orcomplex whose structure is unknown.

Structural information about a portion of any crystallized molecule orcomplex that is sufficiently structurally similar to a portion of apolypeptide of the invention may be resolved by this method. In additionto a molecule that shares one or more structural features with apolypeptide of the invention, a molecule that has similar bioactivity,such as the same catalytic activity, substrate specificity or ligandbinding activity as a polypeptide of the invention, may also besufficiently structurally similar to a polypeptide of the invention topermit use of the structure coordinates for a polypeptide of theinvention to solve its crystal structure.

In another aspect, the method of molecular replacement is utilized toobtain structural information about a complex containing a polypeptideof the invention, such as a complex between a modulator and apolypeptide of the invention (or a domain, fragment, ortholog, homologetc. thereof). In certain instances, the complex includes a polypeptideof the invention (or a domain, fragment, ortholog, homolog etc. thereof)co-complexed with a modulator. For example, in one embodiment, thepresent invention contemplates a method for making a crystallizedcomplex comprising a polypeptide of the invention, or a fragmentthereof, and a compound having a molecular weight of less than 5 kDa,the method comprising: (a) crystallizing a polypeptide of the inventionsuch that the crystals will diffract x-rays to a resolution of 3.5 Å orbetter; and (b) soaking the crystal in a solution comprising thecompound having a molecular weight of less than 5 kDa, thereby producinga crystallized complex comprising the polypeptide and the compound.

Using homology modeling, a computer model of a structural homolog orother polypeptide can be built or refined without crystallizing themolecule. For example, in another aspect, the present invention providesa computer-assisted method for homology modeling a structural homolog ofa polypeptide of the invention including: aligning the amino acidsequence of a known or suspected structural homolog with the amino acidsequence of a polypeptide of the invention and incorporating thesequence of the homolog into a model of a polypeptide of the inventionderived from atomic structure coordinates to yield a preliminary modelof the homolog; subjecting the preliminary model to energy minimizationto yield an energy minimized model; remodeling regions of the energyminimized model where stereochemistry restraints are violated to yield afinal model of the homolog.

In another embodiment, the present invention contemplates a method fordetermining the crystal structure of a homolog of a polypeptide havingSEQ ID NO: 2 or SEQ ID NO: 4, or equivalent thereof, the methodcomprising: (a) providing the three dimensional structure of acrystallized polypeptide having SEQ ID NO: 2 or SEQ ID NO: 4, or afragment thereof; (b) obtaining crystals of a homologous polypeptidecomprising an amino acid sequence that is at least 80% identical to theamino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4 such thatthe three dimensional structure of the crystallized homologouspolypeptide may be determined to a resolution of 3.5 Å or better; and(c) determining the three dimensional structure of the crystallizedhomologous polypeptide by x-ray crystallography based on the atomiccoordinates of the three dimensional structure provided in step (a). Incertain instances of the foregoing method, the atomic coordinates forthe homologous polypeptide have a root mean square deviation from thebackbone atoms of the polypeptide having SEQ ID NO: 2 or SEQ ID NO: 4,or a fragment thereof, of not more than 1.5 Å for all backbone atomsshared in common with the homologous polypeptide and the polypeptidehaving SEQ ID NO: 2 or SEQ ID NO: 4, or a fragment thereof.

(vi) NMR Analysis Using X-ray Structural Data

In another aspect, the structural coordinates of a known crystalstructure may be applied to nuclear magnetic resonance data to determinethe three dimensional structures of polypeptides with uncharacterized orincompletely characterized structure. (See for example, Wuthrich, 1986,John Wiley and Sons, New York: 176-199; Pflugrath et al., 1986, J.Molecular Biology 189: 383-386; Kline et al., 1986 J. Molecular Biology189:377-382). While the secondary structure of a polypeptide may oftenbe determined by NMR data, the spatial connections between individualpieces of secondary structure are not as readily determined. Thestructural coordinates of a polypeptide defined by x-ray crystallographycan guide the NMR spectroscopist to an understanding of the spatialinteractions between secondary structural elements in a polypeptide ofrelated structure. Information on spatial interactions between secondarystructural elements can greatly simplify NOE data from two-dimensionalNMR experiments. In addition, applying the structural coordinates afterthe determination of secondary structure by NMR techniques simplifiesthe assignment of NOE's relating to particular amino acids in thepolypeptide sequence.

In an embodiment, the invention relates to a method of determining threedimensional structures of polypeptides with unknown structures, byapplying the structural coordinates of a crystal of the presentinvention to nuclear magnetic resonance data of the unknown structure.This method comprises the steps of: (a) determining the secondarystructure of an unknown structure using NMR data; and (b) simplifyingthe assignment of through-space interactions of amino acids. The term“through-space interactions” defines the orientation of the secondarystructural elements in the three dimensional structure and the distancesbetween amino acids from different portions of the amino acid sequence.The term “assignment” defines a method of analyzing NMR data andidentifying which amino acids give rise to signals in the NMR spectrum.

For all of this section on x-ray crystallography, see also Brooks et al.(1983) J Comput Chem 4:187-217; Weiner et al (1981) J. Comput. Chem.106: 765; Eisenfield et al. (1991) Am J Physiol 261:C376-386; Lybrand(1991) J Pharm Belg 46:49-54; Froimowitz (1990) Biotechniques 8:640-644;Burbam et al. (1990) Proteins 7:99-111; Pedersen (1985) Environ HealthPerspect 61:185-190; and Kini et al. (1991) J Biomol Struct Dyn9:475-488; Ryckaert et al. (1977) J Comput Phys 23:327; Van Gunsteren etal. (1977) Mol Phys 34:1311; Anderson (1983) J Comput Phys 52:24; J.Mol. Biol. 48: 442-453, 1970; Dayhoff et al., Meth. Enzymol. 91:524-545, 1983; Henikoff and Henikoff, Proc. Nat. Acad. Sci. USA 89:10915-10919, 1992; J. Mol. Biol. 233: 716-738, 1993; Methods inEnzymology, Volume 276, Macromolecular crystallography, Part A, ISBN0-12-182177-3 and Volume 277, Macromolecular crystallography, Part B,ISBN 0-12-182178-1, Eds. Charles W. Carter, Jr. and Robert M. Sweet(1997), Academic Press, San Diego; Pfuetzner, et al., J. Biol. Chem.272: 430-434 (1997).

6. Interacting Proteins

The present invention also provides methods for isolating specificprotein interactors of a polypeptide of the invention, and complexescomprising a polypeptide of the invention and one or more interactingproteins. In one aspect, the present invention contemplates an isolatedprotein complex comprising a polypeptide of the invention and at leastone protein that interacts with the polypeptide of the invention. Theprotein may be naturally-occurring. The interacting protein may be of E.faecalis origin. Alternatively, the interacting protein may be ofmammalian origin or human origin. Either the polypeptide of theinvention or the interacting protein or both may be a fusion protein.

The present invention contemplates a method for identifying a proteincapable of interacting with a polypeptide of the invention or a fragmentthereof, the method comprising: (a) exposing a sample to a solidsubstrate coupled to a polypeptide of the invention or a fragmentthereof under conditions which promote protein-protein interactions; (b)washing the solid substrate so as to remove any polypeptides interactingnon-specifically with the polypeptide or fragment; (c) eluting thepolypeptides which specifically interact with the polypeptide orfragment; and (d) identifying the interacting protein. The sample may bean extract of E. faecalis, a mammalian cell extract, a human cellextract, a purified protein (or a fragment thereof), or a mixture ofpurified proteins (or fragments thereof). The interacting protein may beidentified by a number of methods, including mass spectrometry orprotein sequencing.

In another aspect, the present invention contemplates a method foridentifying a protein capable of interacting with a polypeptide ofpresent invention or a fragment thereof, the method comprising: (a)subjecting a sample to protein-affinity chromatography on multiplecolumns, the columns having a polypeptide of the invention or a fragmentthereof coupled to the column matrix in varying concentrations, andeluting bound components of the extract from the columns; (b) separatingthe components to isolate a polypeptide capable of interacting with thepolypeptide or fragment; and (c) analyzing the interacting protein bymass spectrometry to identify the interacting protein. In certaininstances, the foregoing method will use polyacrylamide gelelectrophoresis without SDS.

In another aspect, the present invention contemplates a method foridentifying a protein capable of interacting with a polypeptide of theinvention, the method comprising: (a) subjecting a cellular extract orextracellular fluid to protein-affinity chromatography on multiplecolumns, the columns having a polypeptide of the invention or a fragmentthereof coupled to the column matrix in varying concentrations, andeluting bound components of the extract from the columns; (b)gel-separating the components to isolate an interacting protein; whereinthe interacting protein is observed to vary in amount in direct relationto the concentration of coupled polypeptide or fragment; (c) digestingthe interacting protein to give corresponding peptides; (d) analyzingthe peptides by MALDI-TOF mass spectrometry or post source decay todetermine the peptide masses; and (d) performing correlative databasesearches with the peptide, or peptide fragment, masses, whereby theinteracting protein is identified based on the masses of the peptides orpeptide fragments. The foregoing method may include the further step ofincluding the identifies of any interacting proteins into a relationaldatabase.

In another aspect, the invention further contemplates a method foridentifying modulators of a protein complex, the method comprising: (a)contacting a protein complex comprising a polypeptide of the inventionand an interacting protein with one or more test compounds; and (b)determining the effect of the test compound on (i) the activity of theprotein complex, (ii) the amount of the protein complex, (iii) thestability of the protein complex, (iv) the conformation of the proteincomplex, (v) the activity of at least one polypeptide included in theprotein complex, (vi) the conformation of at least one polypeptideincluded in the protein complex, (vii) the intracellular localization ofthe protein complex or a component thereof, (viii) the transcriptionlevel of a gene dependent on the complex, and/or (ix) the level ofsecond messenger levels in a cell; thereby identifying modulators of theprotein complex. The foregoing method may be carried out in vitro or invivo as appropriate.

Typically, it will be desirable to immobilize a polypeptide of theinvention to facilitate separation of complexes comprising a polypeptideof the invention from uncomplexed forms of the interacting proteins, aswell as to accommodate automation of the assay. The polypeptide of theinvention, or ligand, may be immobilized onto a solid support (e.g.,column matrix, microtiter plate, slide, etc.). In certain embodiments,the ligand may be purified. In certain instances, a fusion protein maybe provided which adds a domain that permits the ligand to be bound to asupport.

In various in vitro embodiments, the set of proteins engaged in aprotein-protein interaction comprises a cell extract, a clarified cellextract, or a reconstituted protein mixture of at least semi-purifiedproteins. By semi-purified, it is meant that the proteins utilized inthe reconstituted mixture have been previously separated from othercellular or viral proteins. For instance, in contrast to cell lysates,the proteins involved in a protein-protein interaction are present inthe mixture to at least about 50% purity relative to all other proteinsin the mixture, and more preferably are present in greater, even 90-95%,purity. In certain embodiments of the subject method, the reconstitutedprotein mixture is derived by mixing highly purified proteins such thatthe reconstituted mixture substantially lacks other proteins (such as ofcellular or viral origin) which might interfere with or otherwise alterthe ability to measure activity resulting from the given protein-proteininteraction.

Complex formation involving a polypeptide of the invention and anothercomponent polypeptide or a substrate polypeptide, may be detected by avariety of techniques. For instance, modulation in the formation ofcomplexes can be quantitated using, for example, detectably labeledproteins (e.g. radiolabeled, fluorescently labeled, or enzymaticallylabeled), by immunoassay, or by chromatographic detection.

The present invention also provides assays for identifying moleculeswhich are modulators of a protein-protein interaction involving apolypeptide of the invention, or are a modulator of the role of thecomplex comprising a polypeptide of the invention in the infectivity orpathogenicity of E. faecalis. In one embodiment, the assay detectsagents which inhibit formation or stabilization of a protein complexcomprising a polypeptide of the invention and one or more additionalproteins. In another embodiment, the assay detects agents which modulatethe intrinsic biological activity of a protein complex comprising apolypeptide of the invention, such as an enzymatic activity, binding toother cellular components, cellular compartmentalization, signaltransduction, and the like. Such modulators may be used, for example, inthe treatment of E. faecalis related diseases or disorders. In certainembodiments, the compound is a mechanism based inhibitor whichchemically alters one member of a protein-protein interaction involvinga polypeptide of the invention and which is a specific inhibitor of thatmember, e.g. has an inhibition constant about 10-fold, 100-fold, or1000-fold different compared to homologous proteins.

In one embodiment, proteins that interact with a polypeptide of theinvention may be isolated using immunoprecipitation. A polypeptide ofthe invention may be expressed in E. faecalis, or in a heterologoussystem. The cells expressing a polypeptide of the invention are thenlysed under conditions which maintain protein-protein interactions, andcomplexes comprising a polypeptide of the invention are isolated. Forexample, a polypeptide of the invention may be expressed in mammaliancells, including human cells, in order to identify mammalian proteinsthat interact with a polypeptide of the invention and therefore may playa role in E. faecalis infectivity or proliferation. In one embodiment, apolypeptide of the invention is expressed in the cell type for which itis desirable to find interacting proteins. For example, a polypeptide ofthe invention may be expressed in E. faecalis in order to find E.faecalis derived interacting proteins.

In an alternative embodiment, a polypeptide of the invention isexpressed and purified and then mixed with a potential interactingprotein or mixture of proteins to identify complex formation. Thepotential interacting protein may be a single purified or semi-purifiedprotein, or a mixture of proteins, including a mixture of purified orsemi-purified proteins, a cell lysate, a clarified cell lysate, asemi-purified cell lysate, etc.

In certain embodiments, it may be desirable to use a tagged version of apolypeptide of the invention in order to facilitate isolation ofcomplexes from the reaction mixture. Suitable tags forimmunoprecipitation experiments include HA, myc, FLAG, HIS, GST, proteinA, protein G, etc. Immunoprecipitation from a cell lysate or otherprotein mixture may be carried out using an antibody specific for apolypeptide of the invention or using an antibody which recognizes a tagto which a polypeptide of the invention is fused (e.g., anti-HA,anti-myc, anti-FLAG, etc.). Antibodies specific for a variety of tagsare known to the skilled artisan and are commercially available from anumber of sources. In the case where a polypeptide of the invention isfused to a His, GST, or protein A/G tag, immunoprecipitation may becarried out using the appropriate affinity resin (e.g., beadsfunctionalized with Ni, glutathione, Fc region of IgG, etc.). Testcompounds which modulate a protein-protein interaction involving apolypeptide of the invention may be identified by carrying out theimmunoprecipitation reaction in the presence and absence of the testagent and comparing the level and/or activity of the protein complexbetween the two reactions.

In another embodiment, proteins that interact with a polypeptide of theinvention may be identified using affinity chromatography. Some examplesof such chromatography are described in U.S. Ser. No. 09/727,812, filedNov. 30, 2000, and the PCT Application filed Nov. 30, 2001 and entitled“Methods for Systematic Identification of Protein-Protein Interactionsand other Properties”, which claims priority to such U.S. application.

In one aspect, for affinity chromatography using a solid support, apolypeptide of the invention or a fragment thereof may be attached by avariety of means known to those of skill in the art. For example, thepolypeptide may be coupled directly (through a covalent linkage) tocommercially available pre-activated resins as described in Formosa etal., Methods in Enzymology 1991, 208, 24-45; Sopta et al, J. Biol. Chem.1985, 260, 10353-60; Archambault et al., Proc. Natl. Acad. Sci. USA1997, 94, 14300-5. Alternatively, the polypeptide may be tethered to thesolid support through high affinity binding interactions. If thepolypeptide is expressed fused to a tag, such as GST, the fusion tag canbe used to anchor the polypeptide to the matrix support, for exampleSepharose beads containing immobilized glutathione. Solid supports thattake advantage of these tags are commercially available.

In another aspect, the support to which a polypeptide may be immobilizedis a soluble support, which may facilitate certain steps performed inthe methods of the present invention. For example, the soluble supportmay be soluble in the conditions employed to create a bindinginteraction between a target and the polypeptide, and then used underconditions in which it is a solid for elution of the proteins or otherbiological materials that bind to a polypeptide.

The concentration of the coupled polypeptide may have an affect on thesensitivity of the method. In certain embodiments, to detectinteractions most efficiently, the concentration of the polypeptidebound to the matrix should be at least 10-fold higher than the K_(d) ofthe interaction. Thus, the concentration of the polypeptide bound to thematrix should be highest for the detection of the weakestprotein-protein interactions. However, if the concentration of theimmobilized polypeptide is not as high as may be ideal, it may still bepossible to observe protein-protein interactions of interest by, forexample, increasing the concentration of the polypeptide or other moietythat interacts with the coupled polypeptide. The level of detection willof course vary with each different polypeptide, interactor, conditionsof the assay, etc. In certain instances, the interacting protein bindsto the polypeptide with a K_(d) of about 10⁻⁵ M to about 10⁻⁸ M or 10⁻¹⁰M.

In another aspect, the coupling may be done at various ratios of thepolypeptide to the resin. An upper limit of the protein: resin ratio maybe determined by the isoelectric point and the ionic nature of theprotein, although it may be possible to achieve higher polypeptideconcentrations by use of various methods.

In certain embodiments, several concentrations of the polypeptideimmobilized on a solid or soluble support may be used. One advantage ofusing multiple concentrations, although not a requirement, is that onemay be able to obtain an estimate for the strength of theprotein-protein interaction that is observed in the affinitychromatography experiment. Another advantage of using multipleconcentrations is that a binding curve which has the proper shape mayindicate that the interaction that is observed is biologically importantrather than a spurious interaction with denatured protein.

In one example of such an embodiment, a series of columns may beprepared with varying concentrations of polypeptide (mg polypeptide/mlresin volume). The number of columns employed may be between 2 to 8, 10,12, 15, 25 or more, each with a different concentration of attachedpolypeptide. Larger numbers of columns may be used if appropriate forthe polypeptide being examined, and multiple columns may be used withthe same concentration as any methods may require. In certainembodiments, 4 to 6 columns are prepared with varying concentrations ofpolypeptide. In another aspect of this embodiment, two control columnsmay be prepared: one that contains no polypeptide and a second thatcontains the highest concentration of polypeptide but is not treatedwith extract. After elution of the columns and separation of the eluentcomponents (by one of the methods described below), it may be possibleto distinguish the interacting proteins (if any) from the non-specificbound proteins as follows. The concentration of the interactingproteins, as determined by the intensity of the band on the gel, willincrease proportionally to the increase in polypeptide concentration butwill be missing from the second control column. This allows for theidentification of unknown interacting proteins.

The method of the invention may be used for small-scale analysis. Avariety of column sizes, types, and geometries may be used. In addition,other vessel shapes and sizes having a smaller scale than is usuallyfound in laboratory experiments may be used as well, including aplurality of wells in a plate. For high throughput analysis, it isadvantageous to use small volumes, from about 20, 30, 50, 80 or 100 μl.Larger or small volumes may be used, as necessary, and it may bepossible to achieve high throughput analysis using them. The entireaffinity chromatography procedure may be automated by assembling themicro-columns into an array (e.g. with 96 micro-column arrays).

A variety of materials may be used as the source of potentialinteracting proteins. In one embodiment, a cellular extract orextracellular fluid may be used. The choice of starting material for theextract may be based upon the cell or tissue type or type of fluid thatwould be expected to contain proteins that interact with the targetprotein. Micro-organisms or other organisms are grown in a medium thatis appropriate for that organism and can be grown in specific conditionsto promote the expression of proteins that may interact with the targetprotein. Exemplary starting material that may be used to make a suitableextract are: 1) one or more types of tissue derived from an animal,plant, or other multi-cellular organism, 2) cells grown in tissueculture that were derived from an animal or human, plant or othersource, 3) micro-organisms grown in suspension or non-suspensioncultures, 4) virus-infected cells, 5) purified organelles (including,but not restricted to nuclei, mitochondria, membranes, Golgi,endoplasmic reticulum, lysosomes, or peroxisomes) prepared bydifferential centrifugation or another procedure from animal, plant orother kinds of eukaryotic cells, 6) serum or other bodily fluidsincluding, but not limited to, blood, urine, semen, synovial fluid,cerebrospinal fluid, amniotic fluid, lymphatic fluid or interstitialfluid. In other embodiments, a total cell extract may not be the optimalsource of interacting proteins. For example, if the ligand is known toact in the nucleus, a nuclear extract can provide a 10-fold enrichmentof proteins that are likely to interact with the ligand. In addition,proteins that are present in the extract in low concentrations may beenriched using another chromatographic method to fractionate the extractbefore screening various pools for an interacting protein.

Extracts are prepared by methods known to those of skill in the art. Theextracts may be prepared at a low temperature (e.g., 4° C.) in order toretard denaturation or degradation of proteins in the extract. The pH ofthe extract may be adjusted to be appropriate for the body fluid ortissue, cellular, or organellar source that is used for the procedure(e.g. pH 7-8 for cytosolic extracts from mammals, but low pH forlysosomal extracts). The concentration of chaotropic or non-chaotropicsalts in the extracting solution may be adjusted so as to extract theappropriate sets of proteins for the procedure. Glycerol may be added tothe extract, as it aids in maintaining the stability of many proteinsand also reduces background non-specific binding. Both the lysis bufferand column buffer may contain protease inhibitors to minimizeproteolytic degradation of proteins in the extract and to protect thepolypeptide. Appropriate co-factors that could potentially interact withthe interacting proteins may be added to the extracting solution. One ormore nucleases or another reagent may be added to the extract, ifappropriate, to prevent protein-protein interactions that are mediatedby nucleic acids. Appropriate detergents or other agents may be added tothe solution, if desired, to extract membrane proteins from the cells ortissue. A reducing agent (e.g. dithiothreitol or 2-mercaptoethanol orglutathione or other agent) may be added. Trace metals or a chelatingagent may be added, if desired, to the extracting solution.

Usually, the extract is centrifuged in a centrifuge or ultracentrifugeor filtered to provide a clarified supernatant solution. Thissupernatant solution may be dialyzed using dialysis tubing, or anotherkind of device that is standard in the art, against a solution that issimilar to, but may not be identical with, the solution that was used tomake the extract. The extract is clarified by centrifugation orfiltration again immediately prior to its use in affinitychromatography.

In some cases, the crude lysate will contain small molecules that caninterfere with the affinity chromatography. This can be remedied byprecipitating proteins with ammonium sulfate, centrifugation of theprecipitate, and re-suspending the proteins in the affinity columnbuffer followed by dialysis. An additional centrifugation of the samplemay be needed to remove any particulate matter prior to application tothe affinity columns.

The amount of cell extract applied to the column may be important forany embodiment. If too little extract is applied to the column and theinteracting protein is present at low concentration, the level ofinteracting protein retained by the column may be difficult to detect.Conversely, if too much extract is applied to the column, protein mayprecipitate on the column or competition by abundant interactingproteins for the limited amount of protein ligand may result in adifficulty in detecting minor species.

The columns functionalized with a polypeptide of the invention areloaded with protein extract from an appropriate source that has beendialyzed against a buffer that is consistent with the nature of theexpected interaction. The pH, salt concentrations and the presence orabsence of reducing and chelating agents, trace metals, detergents, andco-factors may be adjusted according to the nature of the expectedinteraction. Most commonly, the pH and the ionic strength are chosen soas to be close to physiological for the source of the extract. Theextract is most commonly loaded under gravity onto the columns at a flowrate of about 4-6 column volumes per hour, but this flow rate can beadjusted for particular circumstances in an automated procedure.

The volume of the extract that is loaded on the columns can be variedbut is most commonly equivalent to about 5 to 10 column volumes. Whenlarge volumes of extract are loaded on the columns, there is often animprovement in the signal-to-noise ratio because more protein from theextract is available to bind to the protein ligand, whereas thebackground binding of proteins from the extract to the solid supportsaturates with low amounts of extract.

A control column may be included that contains the highest concentrationof protein ligand, but buffer rather than extract is loaded onto thiscolumn. The elutions (eluates) from this column will contain polypeptidethat failed to be attached to the column in a covalent manner, but noproteins that are derived from the extract.

The columns may be washed with a buffer appropriate to the nature of theinteraction being analyzed, usually, but not necessarily, the same asthe loading buffer. An elution buffer with an appropriate pH, glycerol,and the presence or absence of reducing agent, chelating agent,cofactors, and detergents are all important considerations. The columnsmay be washed with anywhere from about 5 to 20 column volumes of eachwash buffer to eliminate unbound proteins from the natural extract. Theflow rate of the wash is usually adjusted to about 4 to 6 column volumesper hour by using gravity or an automated procedure, but other flowrates are possible in specific circumstances.

In order to elute the proteins that have been retained by the column,the interactions between the extract proteins and the column ligandshould be disrupted. This is performed by eluting the column with asolution of salt or detergent. Retention of activity by the elutedproteins may require the presence of glycerol and a buffer ofappropriate pH, as well as proper choices of ionic strength and thepresence or absence of appropriate reducing agent, chelating agent,trace metals, cofactors, detergents, chaotropic agents, and otherreagents. If physical identification of the bound proteins is theobjective, the elution may be performed sequentially, first with bufferof high ionic strength and then with buffer containing a proteindenaturant, most commonly, but not restricted to sodium dodecyl sulfate(SDS), urea, or guanidine hydrochloride. In certain instances, thecolumn is eluted with a protein denaturant, particularly SDS, forexample as a 1% SDS solution. Using only the SDS wash, and omitting thesalt wash, may result in SDS-gels that have higher resolution (sharperbands with less smearing). Also, using only the SDS wash results in halfas many samples to analyze. The volume of the eluting solution may bevaried but is normally about 2 to 4 column volumes. For 20 ml columns,the flow rate of the eluting procedures are most commonly about 4 to 6column volumes per hour, under gravity, but can be varied in anautomated procedure.

The proteins from the extract that were bound to and are eluted from theaffinity columns may be most easily resolved for identification by anelectrophoresis procedure, but this procedure may be modified, replacedby another suitable method, or omitted. Any of the denaturing ornon-denaturing electrophoresis procedures that are standard in the artmay be used for this purpose, including SDS-PAGE, gradient gels,capillary electrophoresis, and two-dimensional gels with isoelectricfocusing in the first dimension and SDS-PAGE in the second. Typically,the individual components in the column eluent are separated bypolyacrylamide gel electrophoresis.

After electrophoresis, protein bands or spots may be visualized usingany number of methods know to those of skill in the art, includingstaining techniques such as Coomassie blue or silver staining, or someother agent that is standard in the art. Alternatively, autoradiographycan be used for visualizing proteins isolated from organisms cultured onmedia containing a radioactive label, for example ³⁵SO₄ ²⁻ or³⁵[S]methionine, that is incorporated into the proteins. The use ofradioactively labeled extract allows a distinction to be made betweenextract proteins that were retained by the column and proteolyticfragments of the ligand that may be released from the column.

Protein bands that are derived from the extract (i.e. it did not elutefrom the control column that was not loaded with protein from theextract) and bound to an experimental column that contained polypeptidecovalently attached to the solid support, and did not bind to a controlcolumn that did not contain any polypeptide, may be excised from thestained electrophoretic gel and further characterized.

To identify the protein interactor by mass spectrometry, it may bedesirable to reduce the disulfide bonds of the protein followed byalkylation of the free thiols prior to digestion of the protein withprotease. The reduction may be performed by treatment of the gel slicewith a reducing agent, for example with dithiothreitol, whereupon, theprotein is alkylated by treating the gel slice with a suitablealkylating agent, for example iodoacetamide.

Prior to analysis by mass spectrometry, the protein may be chemically orenzymatically digested. The protein sample in the gel slice may besubjected to in-gel digestion. Shevchenko A. et al., Mass SpectrometricSequencing of Proteins from Silver Stained Polyacrylamide Gels.Analytical Chemistry 1996, 58, 850-858. One method of digestion is bytreatment with the enzyme trypsin. The resulting peptides are extractedfrom the gel slice into a buffer.

The peptide fragments may be purified, for example by use ofchromatography. A solid support that differentially binds the peptidesand not the other compounds derived from the gel slice, the proteasereaction or the peptide extract may be used. The peptides may be elutedfrom the solid support into a small volume of a solution that iscompatible with mass spectrometry (e.g. 50% acetonitrile/0.1%trifluoroacetic acid).

The preparation of a protein sample from a gel slice that is suitablefor mass spectrometry may also be done by an automated procedure.

Peptide samples derived from gel slices may be analyzed by any one of avariety of techniques in mass spectrometry as further described above.This technique may be used to assign function to an unknown proteinbased upon the known function of the interacting protein in the same ora homologous/orthologous organism.

Eluates from the affinity chromatography columns may also be analyzeddirectly without resolution by electrophoretic methods, by proteolyticdigestion with a protease in solution, followed by applying theproteolytic digestion products to a reverse phase column and eluting thepeptides from the column.

In yet another embodiment, proteins that interact with a polypeptide ofthe invention may be identified using an interaction trap assay (seealso, U.S. Pat. No. 5,283,317; Zervos et al. (1993) Cell 72:223-232;Madura et al. (1993) J Biol Chem 268:12046-12054; Bartel et al. (1993)Biotechniques 14:920-924; and Iwabuchi et al. (1993) Oncogene8:1693-1696).

In another embodiment, a method of the present invention makes use ofchimeric genes which express hybrid proteins. To illustrate, a firsthybrid gene comprises the coding sequence for a DNA-binding domain of atranscriptional activator fused in frame to the coding sequence for a“bait” protein, e.g., a polypeptide of the invention of sufficientlength to bind to a potential interacting protein. The second hybridprotein encodes a transcriptional activation domain fused in frame to agene encoding a “fish” protein, e.g., a potential interacting protein ofsufficient length to interact with a polypeptide of the inventionportion of the bait fusion protein. If the bait and fish proteins areable to interact, e.g., form a protein-protein interaction, they bringinto close proximity the two domains of the transcriptional activator.This proximity causes transcription of a reporter gene which is operablylinked to a transcriptional regulatory site responsive to thetranscriptional activator, and expression of the reporter gene can bedetected and used to score for the interaction of the bait and fishproteins.

In accordance with the present invention, the method includes providinga host cell, typically a yeast cell, e.g., Kluyverei lactis,Schizosaccharomyces pombe, Ustilago maydis, Saccharomyces cerevisiae,Neurospora crassa, Aspergillus niger, Aspergillus nidulans, Pichiapastoris, Candida tropicalis, and Hansenula polymorpha, though mostpreferably S cerevisiae or S. pombe. The host cell contains a reportergene having a binding site for the DNA-binding domain of atranscriptional activator used in the bait protein, such that thereporter gene expresses a detectable gene product when the gene istranscriptionally activated. The first chimeric gene may be present in achromosome of the host cell, or as part of an expression vector.

The host cell also contains a first chimeric gene which is capable ofbeing expressed in the host cell. The gene encodes a chimeric protein,which comprises (a) a DNA-binding domain that recognizes the responsiveelement on the reporter gene in the host cell, and (b) a bait protein(e.g., a polypeptide of the invention).

A second chimeric gene is also provided which is capable of beingexpressed in the host cell, and encodes the “fish” fusion protein. Inone embodiment, both the first and the second chimeric genes areintroduced into the host cell in the form of plasmids. Preferably,however, the first chimeric gene is present in a chromosome of the hostcell and the second chimeric gene is introduced into the host cell aspart of a plasmid.

The DNA-binding domain of the first hybrid protein and thetranscriptional activation domain of the second hybrid protein may bederived from transcriptional activators having separable DNA-binding andtranscriptional activation domains. For instance, these separateDNA-binding and transcriptional activation domains are known to be foundin the yeast GALA protein, and are known to be found in the yeast GCN4and ADR1 proteins. Many other proteins involved in transcription alsohave separable binding and transcriptional activation domains which makethem useful for the present invention, and include, for example, theLexA and VP16 proteins. It will be understood that other (substantially)transcriptionally-inert DNA-binding domains may be used in the subjectconstructs; such as domains of ACE1, λcI, lac repressor, jun or fos. Inanother embodiment, the DNA-binding domain and the transcriptionalactivation domain may be from different proteins. The use of a LexA DNAbinding domain provides certain advantages. For example, in yeast, theLexA moiety contains no activation function and has no known affect ontranscription of yeast genes. In addition, use of LexA allows controlover the sensitivity of the assay to the level of interaction (see, forexample, the Brent et al. PCT publication WO94/10300).

In certain embodiments, any enzymatic activity associated with the baitor fish proteins is inactivated, e.g., dominant negative or othermutants of a protein-protein interaction component can be used.

Continuing with the illustrative example, a polypeptide of theinvention-mediated interaction, if any, between the bait and fish fusionproteins in the host cell, causes the activation domain to activatetranscription of the reporter gene. The method is carried out byintroducing the first chimeric gene and the second chimeric gene intothe host cell, and subjecting that cell to conditions under which thebait and fish fusion proteins and are expressed in sufficient quantityfor the reporter gene to be activated. The formation of a proteincomplex containing a polypeptide of the invention results in adetectable signal produced by the expression of the reporter gene.

In still further embodiments, the protein-protein interaction ofinterest is generated in whole cells, taking advantage of cell culturetechniques to support the subject assay. For example, theprotein-protein interaction of interest can be constituted in aprokaryotic or eukaryotic cell culture system. Advantages to generatingthe protein complex in an intact cell includes the ability to screen forinhibitors of the level or activity of the complex which are functionalin an environment more closely approximating that which therapeutic useof the inhibitor would require, including the ability of the agent togain entry into the cell. Furthermore, certain of the in vivoembodiments of the assay are amenable to high through-put analysis ofcandidate agents.

The components of the protein complex comprising a polypeptide of theinvention can be endogenous to the cell selected to support the assay.Alternatively, some or all of the components can be derived fromexogenous sources. For instance, fusion proteins can be introduced intothe cell by recombinant techniques (such as through the use of anexpression vector), as well as by microinjecting the fusion proteinitself or mRNA encoding the fusion protein. Moreover, in the whole cellembodiments of the subject assay, the reporter gene construct canprovide, upon expression, a selectable marker. Such embodiments of thesubject assay are particularly amenable to high through-put analysis inthat proliferation of the cell can provide a simple measure of theprotein-protein interaction.

The amount of transcription from the reporter gene may be measured usingany method known to those of skill in the art to be suitable. Forexample, specific mRNA expression may be detected using Northern blotsor specific protein product may be identified by a characteristic stain,western blots or an intrinsic activity. In certain embodiments, theproduct of the reporter gene is detected by an intrinsic activityassociated with that product. For instance, the reporter gene may encodea gene product that, by enzymatic activity, gives rise to a detectionsignal based on color, fluorescence, or luminescence.

The interaction trap assay of the invention may also be used to identifytest agents capable of modulating formation of a complex comprising apolypeptide of the invention. In general, the amount of expression fromthe reporter gene in the presence of the test compound is compared tothe amount of expression in the same cell in the absence of the testcompound. Alternatively, the amount of expression from the reporter genein the presence of the test compound may be compared with the amount oftranscription in a substantially identical cell that lacks a componentof the protein-protein interaction involving a polypeptide of theinvention.

7. Antibodies

Another aspect of the invention pertains to antibodies specificallyreactive with a polypeptide of the invention. For example, by usingpeptides based on a polypeptide of the invention, e.g., having an aminoacid sequence of SEQ ID NO: 2 or SEQ ID NO: 4 or an immunogenic fragmentthereof, antisera or monoclonal antibodies may be made using standardmethods. An exemplary immunogenic fragment may contain eight, ten ormore consecutive amino acid residues of SEQ ID NO: 2 or SEQ ID NO: 4.Certain fragments that are predicted to be immunogenic for the subjectamino acid sequences (predicted) are set forth in Table 2 contained inFIG. 7

The term “antibody” as used herein is intended to include fragmentsthereof which are also specifically reactive with a polypeptide of theinvention. Antibodies can be fragmented using conventional techniquesand the fragments screened for utility in the same manner as is suitablefor whole antibodies. For example, F(ab′)₂ fragments can be generated bytreating antibody with pepsin. The resulting F(ab′)₂ fragment can betreated to reduce disulfide bridges to produce Fab′ fragments. Theantibody of the present invention is further intended to includebispecific and chimeric molecules, as well as single chain (scFv)antibodies. Also within the scope of the invention are trimericantibodies, humanized antibodies, human antibodies, and single chainantibodies. All of these modified forms of antibodies as well asfragments of antibodies are intended to be included in the term“antibody”.

In one aspect, the present invention contemplates a purified antibodythat binds specifically to a polypeptide of the invention and which doesnot substantially cross-react with a protein which is less than about80%, or less than about 90%, identical to SEQ ID NO: 2 or SEQ ID NO: 4.In another aspect, the present invention contemplates an arraycomprising a substrate having a plurality of address, wherein at leastone of the addresses has disposed thereon a purified antibody that bindsspecifically to a polypeptide of the invention.

Antibodies may be elicited by methods known in the art. For example, amammal such as a mouse, a hamster or rabbit may be immunized with animmunogenic form of a polypeptide of the invention (e.g., an antigenicfragment which is capable of eliciting an antibody response).Alternatively, immunization may occur by using a nucleic acid of theacid, which presumably in vivo expresses the polypeptide of theinvention giving rise to the immunogenic response observed. Techniquesfor conferring immunogenicity on a protein or peptide includeconjugation to carriers or other techniques well known in the art. Forinstance, a peptidyl portion of a polypeptide of the invention may beadministered in the presence of adjuvant. The progress of immunizationmay be monitored by detection of antibody titers in plasma or serum.Standard ELISA or other immunoassays may be used with the immunogen asantigen to assess the levels of antibodies.

Following immunization, antisera reactive with a polypeptide of theinvention may be obtained and, if desired, polyclonal antibodiesisolated from the serum. To produce monoclonal antibodies, antibodyproducing cells (lymphocytes) may be harvested from an immunized animaland fused by standard somatic cell fusion procedures with immortalizingcells such as myeloma cells to yield hybridoma cells. Such techniquesare well known in the art, and include, for example, the hybridomatechnique (originally developed by Kohler and Milstein, (1975) Nature,256: 495-497), as the human B cell hybridoma technique (Kozbar et al.,(1983) Immunology Today, 4: 72), and the EBV-hybridoma technique toproduce human monoclonal antibodies (Cole et al., (1985) MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96). Hybridomacells can be screened immunochemically for production of antibodiesspecifically reactive with the polypeptides of the invention and themonoclonal antibodies isolated.

Antibodies directed against the polypeptides of the invention can beused to selectively block the action of the polypeptides of theinvention. Antibodies against a polypeptide of the invention may beemployed to treat infections, particularly bacterial infections anddiseases. For example, the present invention contemplates a method fortreating a subject suffering from a E. faecalis related disease ordisorder, comprising administering to an animal having the condition atherapeutically effective amount of a purified antibody that bindsspecifically to a polypeptide of the invention. In another example, thepresent invention contemplates a method for inhibiting SEQ ID NO: 2 orSEQ ID NO: 4 dependent growth or infectivity of E. faecalis, comprisingcontacting E. faecalis with a purified antibody that binds specificallyto a polypeptide of the invention.

In one embodiment, antibodies reactive with a polypeptide of theinvention are used in the immunological screening of cDNA librariesconstructed in expression vectors, such as λgt11, λgt18-23, λZAP, andλORF8. Messenger libraries of this type, having coding sequencesinserted in the correct reading frame and orientation, can producefusion proteins. For instance, λgt11 will produce fusion proteins whoseamino termini consist of β-galactosidase amino acid sequences and whosecarboxy termini consist of a foreign polypeptide. Antigenic epitopes ofa polypeptide of the invention can then be detected with antibodies, as,for example, reacting nitrocellulose filters lifted from phage infectedbacterial plates with an antibody specific for a polypeptide of theinvention. Phage scored by this assay can then be isolated from theinfected plate. Thus, homologs of a polypeptide of the invention can bedetected and cloned from other sources.

Antibodies may be employed to isolate or to identify clones expressingthe polypeptides to purify the polypeptides by affinity chromatography.

In other embodiments, the polypeptides of the invention may be modifiedso as to increase their immunogenicity. For example, a polypeptide, suchas an antigenically or immunologically equivalent derivative, may beassociated, for example by conjugation, with an immunogenic carrierprotein for example bovine serum albumin (BSA) or keyhole limpethaemocyanin (KLH). Alternatively a multiple antigenic peptide comprisingmultiple copies of the protein or polypeptide, or an antigenically orimmunologically equivalent polypeptide thereof may be sufficientlyantigenic to improve immunogenicity so as to obviate the use of acarrier.

In other embodiments, the antibodies of the invention, or variantsthereof, are modified to make them less immunogenic when administered toa subject. For example, if the subject is human, the antibody may be“humanized”; where the complimentarily determining region(s) of thehybridoma-derived antibody has been transplanted into a human monoclonalantibody, for example as described in Jones, P. et al. (1986), Nature321, 522-525 or Tempest et al. (1991) Biotechnology 9, 266-273. Also,transgenic mice, or other mammals, may be used to express humanizedantibodies. Such humanization may be partial or complete.

The use of a nucleic acid of the invention in genetic immunization mayemploy a suitable delivery method such as direct injection of plasmidDNA into muscles (Wolff et al., Hum Mol Genet 1992, 1:363, Manthorpe etal., Hum. Gene Ther. 1963:4, 419), delivery of DNA complexed withspecific protein carriers (Wu et al., J Biol. Chem. 1989: 264, 16985),coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNASUSA, 1986:83, 9551), encapsulation of DNA in various forms of liposomes(Kaneda et al., Science 1989:243, 375), particle bombardment (Tang etal., Nature 1992, 356:152, Eisenbraun et al., DNA Cell Biol 1993,12:791) and in vivo infection using cloned retroviral vectors (Seeger etal., PNAS USA 1984:81, 5849).

8. Diagnostic Assays

The invention further provides a method for detecting the presence of E.faecalis in a biological sample. Detection of E. faecalis in a subject,particularly a mammal, and especially a human, will provide a diagnosticmethod for diagnosis of a E. faecalis related disease or disorder. Ingeneral, the method involves contacting the biological sample with acompound or an agent capable of detecting a polypeptide of the inventionor a nucleic acid of the invention. The term “biological sample” whenused in reference to a diagnostic assay is intended to include tissues,cells and biological fluids isolated from a subject, as well as tissues,cells and fluids present within a subject.

The detection method of the invention may be used to detect the presenceof E. faecalis in a biological sample in vitro as well as in vivo. Forexample, in vitro techniques for detection of a nucleic acid of theinvention include Northern hybridizations and in situ hybridizations. Invitro techniques for detection of polypeptides of the invention includeenzyme linked immunosorbent assays (ELISAs), Western blots,immunoprecipitations, immunofluorescence, radioimmunoassays andcompetitive binding assays. Alternatively, polypeptides of the inventioncan be detected in vivo in a subject by introducing into the subject alabeled antibody specific for a polypeptide of the invention. Forexample, the antibody can be labeled with a radioactive marker whosepresence and location in a subject can be detected by standard imagingtechniques. It may be possible to use all of the diagnostic methodsdisclosed herein for pathogens in addition to E. faecalis.

Nucleic acids for diagnosis may be obtained from an infectedindividual's cells and tissues, such as bone, blood, muscle, cartilage,and skin. Nucleic acids, e.g., DNA and RNA, may be used directly fordetection or may be amplified, e.g., enzymatically by using PCR or otheramplification technique, prior to analysis. Using amplification,characterization of the species and strain of prokaryote present in anindividual, may be made by an analysis of the genotype of the prokaryotegene. Deletions and insertions can be detected by a change in size ofthe amplified product in comparison to the genotype of a referencesequence. Point mutations can be identified by hybridizing a nucleicacid, e.g., amplified DNA, to a nucleic acid of the invention, whichnucleic acid may be labeled. Perfectly matched sequences can bedistinguished from mismatched duplexes by RNase digestion or bydifferences in melting temperatures. DNA sequence differences may alsobe detected by alterations in the electrophoretic mobility of the DNAfragments in gels, with or without denaturing agents, or by direct DNAsequencing. See, e.g. Myers et al., Science, 230: 1242 (1985). Sequencechanges at specific locations also may be revealed by nucleaseprotection assays, such as RNase and S1 protection or a chemicalcleavage method. See, e.g., Cotton et al., Proc. Natl. Acad. Sci., USA,85: 4397-4401 (1985).

Agents for detecting a nucleic acid of the invention, e.g., comprisingthe sequence set forth in SEQ ID NO: 1 or SEQ ID NO: 3, include labeledor labelable nucleic acid probes capable of hybridizing to a nucleicacid of the invention. The nucleic acid probe can comprise, for example,the full length sequence of a nucleic acid of the invention, or anequivalent thereof, or a portion thereof, such as an oligonucleotide ofat least 15, 30, 50, 100, 250 or 500 nucleotides in length andsufficient to specifically hybridize under stringent conditions to SEQID NO: 1 or SEQ ID NO: 3, or the complement thereof. Agents fordetecting a polypeptide of the invention, e.g., comprising an amino acidsequence of SEQ ID NO: 2 or SEQ ID NO: 4, include labeled or labelableantibodies capable of binding to a polypeptide of the invention.Antibodies may be polyclonal, or alternatively, monoclonal. An intactantibody, or a fragment thereof (e.g., Fab or F(ab′)₂) can be used.Labeling the probe or antibody also encompasses direct labeling of theprobe or antibody by coupling (e.g., physically linking) a detectablesubstance to the probe or antibody, as well as indirect labeling of theprobe or antibody by reactivity with another reagent that is directlylabeled. Examples of indirect labeling include detection of a primaryantibody using a fluorescently labeled secondary antibody andend-labeling of a DNA probe with biotin such that it can be detectedwith fluorescently labeled streptavidin.

In certain embodiments, detection of a nucleic acid of the invention ina biological sample involves the use of a probe/primer in a polymerasechain reaction (PCR) (see, e.g. U.S. Pat. Nos. 4,683,195 and 4,683,202),such as anchor PCR or RACE PCR, or, alternatively, in a ligation chainreaction (LCR) (see, e.g., Landegran et al. (1988) Science241:1077-1080; and Nakazawa et al. (1994) PNAS 91:360-364), the latterof which can be particularly useful for distinguishing between orthologsof polynucleotides of the invention (see Abravaya et al. (1995) NucleicAcids Res. 23:675-682). This method can include the steps of collectinga sample of cells from a patient, isolating nucleic acid (e.g., genomic,mRNA or both) from the cells of the sample, contacting the nucleic acidsample with one or more primers which specifically hybridize to anucleic acid of the invention under conditions such that hybridizationand amplification of the polynucleotide (if present) occurs, anddetecting the presence or absence of an amplification product, ordetecting the size of the amplification product and comparing the lengthto a control sample.

In one aspect, the present invention contemplates a method for detectingthe presence of E. faecalis in a sample, the method comprising: (a)providing a sample to be tested for the presence of E. faecalis; (b)contacting the sample with an antibody reactive against eightconsecutive amino acid residues of SEQ ID NO: 2 or SEQ ID NO: 4 underconditions which permit association between the antibody and its ligand;and (c) detecting interaction of the antibody with its ligand, therebydetecting the presence of E. faecalis in the sample.

In another aspect, the present invention contemplates a method fordetecting the presence of E. faecalis in a sample, the methodcomprising: (a) providing a sample to be tested for the presence of E.faecalis; (b) contacting the sample with an antibody that bindsspecifically to a polypeptide of the invention under conditions whichpermit association between the antibody and its ligand; and (c)detecting interaction of the antibody with its ligand, thereby detectingthe presence of E. faecalis in the sample.

In yet another example, the present invention contemplates a method fordiagnosing a patient suffering from a E. faecalis related disease ordisorder, comprising: (a) obtaining a biological sample from a patient;(b) detecting the presence or absence of a polypeptide of the invention,or a nucleic acid encoding a polypeptide of the invention, in thesample; and (c) diagnosing a patient suffering from a E. faecalisrelated disease or disorder based on the presence of a polypeptide ofthe invention, or a nucleic acid encoding a polypeptide of theinvention, in the patient sample.

The diagnostic assays of the invention may also be used to monitor theeffectiveness of an anti-E. faecalis treatment in an individualsuffering from an E. faecalis related disease or disorder. For example,the presence and/or amount of a nucleic acid of the invention or apolypeptide of the invention can be detected in an individual sufferingfrom an E. faecalis related disease or disorder before and aftertreatment with anti-E. faecalis therapeutic agent. Any change in thelevel of a polynucleotide or polypeptide of the invention aftertreatment of the individual with the therapeutic agent can provideinformation about the effectiveness of the treatment course. Inparticular, no change, or a decrease, in the level of a polynucleotideor polypeptide of the invention present in the biological sample willindicate that the therapeutic is successfully combating the E. faecalisrelated disease or disorder.

The invention also encompasses kits for detecting the presence of E.faecalis in a biological sample. For example, the kit can comprise alabeled or labelable compound or agent capable of detecting apolynucleotide or polypeptide of the invention in a biological sample;means for determining the amount of E. faecalis in the sample; and meansfor comparing the amount of E. faecalis in the sample with a standard.The compound or agent can be packaged in a suitable container. The kitcan further comprise instructions for using the kit to detect apolynucleotide or polypeptide of the invention.

9. Drug Discovery

Modulators to polypeptides of the invention and other structurallyrelated molecules, and complexes containing the same, may be identifiedand developed as set forth below and otherwise using techniques andmethods known to those of skill in the art. The modulators of theinvention may be employed, for instance, to inhibit and treat E.faecalis associated diseases or conditions, such as urinary tractinfection, surgical wound infection, bacteremia, intra abdominalinfection, pelvic infection, central nervous system infection,osteomyelitis, pulmonary infection, and endocarditis.

A variety of methods for inhibiting the growth or infectivity of E.faecalis are contemplated by the present invention. For example,exemplary methods involve contacting E. faecalis with a polypeptide ofthe invention that modulates the same or another polypeptide from suchpathogen, a nucleic acid encoding such polypeptide of the invention, ora compound thought or shown to be effective against such pathogen.

For example, in one aspect, the present invention contemplates a methodfor treating a patient suffering from an infection of E. faecalis,comprising administering to the patient an amount of a SEQ ID NO: 2 orSEQ ID NO: 4 inhibitor effective to inhibit the expression and/oractivity of a polypeptide of the invention. In certain instances, theanimal is a human or a livestock animal such as a cow, pig, goat orsheep. The present invention further contemplates a method for treatinga subject suffering from a E. faecalis related disease or disorder,comprising administering to an animal having the condition atherapeutically effective amount of a molecule identified using one ofthe methods of the present invention.

The present invention contemplates making any molecule that is shown tomodulate the activity of a polypeptide of the invention.

In another embodiment, inhibitors, modulators of the subjectpolypeptides, or biological complexes containing them, may be used inthe manufacture of a medicament for any number of uses, including, forexample, treating any disease or other treatable condition of a patient(including humans and animals), and particularly a disease caused by E.faecalis, such as, for example, one of the following: urinary tractinfection, surgical wound infection, bacteremia, intra abdominalinfection, pelvic infection, central nervous system infection,osteomyelitis, pulmonary infection, and endocarditis.

(a) Drug Design

A number of techniques can be used to screen, identify, select anddesign chemical entities capable of associating with polypeptides of theinvention, structurally homologous molecules, and other molecules.Knowledge of the structure for a polypeptide of the invention,determined in accordance with the methods described herein, permits thedesign and/or identification of molecules and/or other modulators whichhave a shape complementary to the conformation of a polypeptide of theinvention, or more particularly, a druggable region thereof. It isunderstood that such techniques and methods may use, in addition to theexact structural coordinates and other information for a polypeptide ofthe invention, structural equivalents thereof described above(including, for example, those structural coordinates that are derivedfrom the structural coordinates of amino acids contained in a druggableregion as described above).

The term “chemical entity,” as used herein, refers to chemicalcompounds, complexes of two or more chemical compounds, and fragments ofsuch compounds or complexes. In certain instances, it is desirable touse chemical entities exhibiting a wide range of structural andfunctional diversity, such as compounds exhibiting different shapes(e.g., flat aromatic rings(s), puckered aliphatic rings(s), straight andbranched chain aliphatics with single, double, or triple bonds) anddiverse functional groups (e.g., carboxylic acids, esters, ethers,amines, aldehydes, ketones, and various heterocyclic rings).

In one aspect, the method of drug design generally includescomputationally evaluating the potential of a selected chemical entityto associate with any of the molecules or complexes of the presentinvention (or portions thereof). For example, this method may includethe steps of (a) employing computational means to perform a fittingoperation between the selected chemical entity and a druggable region ofthe molecule or complex; and (b) analyzing the results of said fittingoperation to quantify the association between the chemical entity andthe druggable region.

A chemical entity may be examined either through visual inspection orthrough the use of computer modeling using a docking program such asGRAM, DOCK, or AUTODOCK (Dunbrack et al., Folding & Design, 2:27-42(1997)). This procedure can include computer fitting of chemicalentities to a target to ascertain how well the shape and the chemicalstructure of each chemical entity will complement or interfere with thestructure of the subject polypeptide (Bugg et al., Scientific American,Dec.: 92-98 (1993); West et al., TIPS, 16:67-74 (1995)). Computerprograms may also be employed to estimate the attraction, repulsion, andsteric hindrance of the chemical entity to a druggable region, forexample. Generally, the tighter the fit (e.g., the lower the sterichindrance, and/or the greater the attractive force) the more potent thechemical entity will be because these properties are consistent with atighter binding constant. Furthermore, the more specificity in thedesign of a chemical entity the more likely that the chemical entitywill not interfere with related proteins, which may minimize potentialside-effects due to unwanted interactions.

A variety of computational methods for molecular design, in which thesteric and electronic properties of druggable regions are used to guidethe design of chemical entities, are known: Cohen et al. (1990) J. Med.Cam. 33: 883-894; Kuntz et al. (1982) J. Mol. Biol. 161: 269-288;DesJarlais (1988) J. Med. Cam. 31: 722-729; Bartlett et al. (1989) Spec.Publ., Roy. Soc. Chem. 78: 182-196; Goodford et al. (1985) J. Med. Cam.28: 849-857; and DesJarlais et al. J. Med. Cam. 29: 2149-2153. Directedmethods generally fall into two categories: (1) design by analogy inwhich 3-D structures of known chemical entities (such as from acrystallographic database) are docked to the druggable region and scoredfor goodness-of-fit; and (2) de novo design, in which the chemicalentity is constructed piece-wise in the druggable region. The chemicalentity may be screened as part of a library or a database of molecules.Databases which may be used include ACD (Molecular Designs Limited), NCI(National Cancer Institute), CCDC (Cambridge Crystallographic DataCenter), CAST (Chemical Abstract Service), Derwent (Derwent InformationLimited), Maybridge (Maybridge Chemical Company Ltd), Aldrich (AldrichChemical Company), DOCK (University of California in San Francisco), andthe Directory of Natural Products (Chapman & Hall). Computer programssuch as CONCORD (Tripos Associates) or DB-Converter (MolecularSimulations Limited) can be used to convert a data set represented intwo dimensions to one represented in three dimensions.

Chemical entities may be tested for their capacity to fit spatially witha druggable region or other portion of a target protein. As used herein,the term “fits spatially” means that the three-dimensional structure ofthe chemical entity is accommodated geometrically by a druggable region.A favorable geometric fit occurs when the surface area of the chemicalentity is in close proximity with the surface area of the druggableregion without forming unfavorable interactions. A favorablecomplementary interaction occurs where the chemical entity interacts byhydrophobic, aromatic, ionic, dipolar, or hydrogen donating andaccepting forces. Unfavorable interactions may be steric hindrancebetween atoms in the chemical entity and atoms in the druggable region.

If a model of the present invention is a computer model, the chemicalentities may be positioned in a druggable region through computationaldocking. If, on the other hand, the model of the present invention is astructural model, the chemical entities may be positioned in thedruggable region by, for example, manual docking. As used herein theterm “docking” refers to a process of placing a chemical entity in closeproximity with a druggable region, or a process of finding low energyconformations of a chemical entity/druggable region complex.

In an illustrative embodiment, the design of potential modulator beginsfrom the general perspective of shape complimentary for the druggableregion of a polypeptide of the invention, and a search algorithm isemployed which is capable of scanning a database of small molecules ofknown three-dimensional structure for chemical entities which fitgeometrically with the target druggable region. Most algorithms of thistype provide a method for finding a wide assortment of chemical entitiesthat are complementary to the shape of a druggable region of the subjectpolypeptide. Each of a set of chemical entities from a particulardata-base, such as the Cambridge Crystallographic Data Bank (CCDB)(Allen et al. (1973) J. Chem. Doc. 13: 119), is individually docked tothe druggable region of a polypeptide of the invention in a number ofgeometrically permissible orientations with use of a docking algorithm.In certain embodiments, a set of computer algorithms called DOCK, can beused to characterize the shape of invaginations and grooves that formthe active sites and recognition surfaces of the druggable region (Kuntzet al. (1982) J. Mol. Biol. 161: 269-288). The program can also search adatabase of small molecules for templates whose shapes are complementaryto particular binding sites of a polypeptide of the invention(DesJarlais et al. (1988) J Med Chem 31: 722-729).

The orientations are evaluated for goodness-of-fit and the best are keptfor further examination using molecular mechanics programs, such asAMBER or CHARMM. Such algorithms have previously proven successful infinding a variety of chemical entities that are complementary in shapeto a druggable region.

Goodford (1985, J Med Chem 28:849-857) and Boobbyer et al. (1989, J MedChem 32:1083-1094) have produced a computer program (GRID) which seeksto determine regions of high affinity for different chemical groups(termed probes) of the druggable region. GRID hence provides a tool forsuggesting modifications to known chemical entities that might enhancebinding. It may be anticipated that some of the sites discerned by GRIDas regions of high affinity correspond to “pharmacophoric patterns”determined inferentially from a series of known ligands. As used herein,a “pharmacophoric pattern” is a geometric arrangement of features ofchemical entities that is believed to be important for binding. Attemptshave been made to use pharmacophoric patterns as a search screen fornovel ligands (Jakes et al. (1987) J Mol Graph 5:4148; Brint et al.(1987) J Mol Graph 5:49-56; Jakes et al. (1986) J Mol Graph 4:12-20).

Yet a further embodiment of the present invention utilizes a computeralgorithm such as CLIX which searches such databases as CCDB forchemical entities which can be oriented with the druggable region in away that is both sterically acceptable and has a high likelihood ofachieving favorable chemical interactions between the chemical entityand the surrounding amino acid residues. The method is based oncharacterizing the region in terms of an ensemble of favorable bindingpositions for different chemical groups and then searching fororientations of the chemical entities that cause maximum spatialcoincidence of individual candidate chemical groups with members of theensemble. The algorithmic details of CLIX is described in Lawrence etal. (1992) Proteins 12:3141.

In this way, the efficiency with which a chemical entity may bind to orinterfere with a druggable region may be tested and optimized bycomputational evaluation. For example, for a favorable association witha druggable region, a chemical entity must preferably demonstrate arelatively small difference in energy between its bound and fine states(i.e., a small deformation energy of binding). Thus, certain, moredesirable chemical entities will be designed with a deformation energyof binding of not greater than about 10 kcal/mole, and more preferably,not greater than 7 kcal/mole. Chemical entities may interact with adruggable region in more than one conformation that is similar inoverall binding energy. In those cases, the deformation energy ofbinding is taken to be the difference between the energy of the freeentity and the average energy of the conformations observed when thechemical entity binds to the target.

In this way, the present invention provides computer-assisted methodsfor identifying or designing a potential modulator of the activity of apolypeptide of the invention including: supplying a computer modelingapplication with a set of structure coordinates of a molecule orcomplex, the molecule or complex including at least a portion of adruggable region from a polypeptide of the invention; supplying thecomputer modeling application with a set of structure coordinates of achemical entity; and determining whether the chemical entity is expectedto bind to the molecule or complex, wherein binding to the molecule orcomplex is indicative of potential modulation of the activity of apolypeptide of the invention.

In another aspect, the present invention provides a computer-assistedmethod for identifying or designing a potential modulator to apolypeptide of the invention, supplying a computer modeling applicationwith a set of structure coordinates of a molecule or complex, themolecule or complex including at least a portion of a druggable regionof a polypeptide of the invention; supplying the computer modelingapplication with a set of structure coordinates for a chemical entity;evaluating the potential binding interactions between the chemicalentity and active site of the molecule or molecular complex;structurally modifying the chemical entity to yield a set of structurecoordinates for a modified chemical entity, and determining whether themodified chemical entity is expected to bind to the molecule or complex,wherein binding to the molecule or complex is indicative of potentialmodulation of the polypeptide of the invention.

In one embodiment, a potential modulator can be obtained by screening apeptide library (Scott and Smith, Science, 249:386-390 (1990); Cwirla etal., Proc. Natl. Acad. Sci., 87:6378-6382 (1990); Devlin et al.,Science, 249:404-406 (1990)). A potential modulator selected in thismanner could then be systematically modified by computer modelingprograms until one or more promising potential drugs are identified.Such analysis has been shown to be effective in the development of HIVprotease inhibitors (Lam et al., Science 263:380-384 (1994); Wlodawer etal., Ann. Rev. Biochem. 62:543-585 (1993); Appelt, Perspectives in DrugDiscovery and Design 1:23-48 (1993); Erickson, Perspectives in DrugDiscovery and Design 1:109-128 (1993)). Alternatively a potentialmodulator may be selected from a library of chemicals such as those thatcan be licensed from third parties, such as chemical and pharmaceuticalcompanies. A third alternative is to synthesize the potential modulatorde novo.

For example, in certain embodiments, the present invention provides amethod for making a potential modulator for a polypeptide of theinvention, the method including synthesizing a chemical entity or amolecule containing the chemical entity to yield a potential modulatorof a polypeptide of the invention, the chemical entity having beenidentified during a computer-assisted process including supplying acomputer modeling application with a set of structure coordinates of amolecule or complex, the molecule or complex including at least onedruggable region from a polypeptide of the invention; supplying thecomputer modeling application with a set of structure coordinates of achemical entity; and determining whether the chemical entity is expectedto bind to the molecule or complex at the active site, wherein bindingto the molecule or complex is indicative of potential modulation. Thismethod may further include the steps of evaluating the potential bindinginteractions between the chemical entity and the active site of themolecule or molecular complex and structurally modifying the chemicalentity to yield a set of structure coordinates for a modified chemicalentity, which steps may be repeated one or more times.

Once a potential modulator is identified, it can then be tested in anystandard assay for the macromolecule depending of course on themacromolecule, including in high throughput assays. Further refinementsto the structure of the modulator will generally be necessary and can bemade by the successive iterations of any and/or all of the stepsprovided by the particular screening assay, in particular furtherstructural analysis by e.g., ¹⁵N NMR relaxation rate determinations orx-ray crystallography with the modulator bound to the subjectpolypeptide. These studies may be performed in conjunction withbiochemical assays.

Once identified, a potential modulator may be used as a model structure,and analogs to the compound can be obtained. The analogs are thenscreened for their ability to bind the subject polypeptide. An analog ofthe potential modulator might be chosen as a modulator when it binds tothe subject polypeptide with a higher binding affinity than thepredecessor modulator.

In a related approach, iterative drug design is used to identifymodulators of a target protein. Iterative drug design is a method foroptimizing associations between a protein and a modulator by determiningand evaluating the three dimensional structures of successive sets ofprotein/modulator complexes. In iterative drug design, crystals of aseries of protein/modulator complexes are obtained and then thethree-dimensional structures of each complex is solved. Such an approachprovides insight into the association between the proteins andmodulators of each complex. For example, this approach may beaccomplished by selecting modulators with inhibitory activity, obtainingcrystals of this new protein/modulator complex, solving the threedimensional structure of the complex, and comparing the associationsbetween the new protein/modulator complex and previously solvedprotein/modulator complexes. By observing how changes in the modulatoraffected the protein/modulator associations, these associations may beoptimized.

In addition to designing and/or identifying a chemical entity toassociate with a druggable region, as described above, the sametechniques and methods may be used to design and/or identify chemicalentities that either associate, or do not associate, with affinityregions, selectivity regions or undesired regions of protein targets. Bysuch methods, selectivity for one or a few targets, or alternatively formultiple targets, from the same species or from multiple species, can beachieved.

For example, a chemical entity may be designed and/or identified forwhich the binding energy for one druggable region, e.g., an affinityregion or selectivity region, is more favorable than that for anotherregion, e.g., an undesired region, by about 20%, 30%, 50% to about 60%or more. It may be the case that the difference is observed between (a)more than two regions, (b) between different regions (selectivity,affinity or undesirable) from the same target, (c) between regions ofdifferent targets, (d) between regions of homologs from differentspecies, or (e) between other combinations. Alternatively, thecomparison may be made by reference to the K_(d), usually the apparentK_(d), of said chemical entity with the two or more regions in question.

In another aspect, prospective modulators are screened for binding totwo nearby druggable regions on a target protein. For example, amodulator that binds a first region of a target polypeptide does notbind a second nearby region. Binding to the second region can bedetermined by monitoring changes in a different set of amide chemicalshifts in either the original screen or a second screen conducted in thepresence of a modulator (or potential modulator) for the first region.From an analysis of the chemical shift changes, the approximate locationof a potential modulator for the second region is identified.Optimization of the second modulator for binding to the region is thencarried out by screening structurally related compounds (e.g., analogsas described above). When modulators for the first region and the secondregion are identified, their location and orientation in the ternarycomplex can be determined experimentally. On the basis of thisstructural information, a linked compound, e.g., a consolidatedmodulator, is synthesized in which the modulator for the first regionand the modulator for the second region are linked. In certainembodiments, the two modulators are covalently linked to form aconsolidated modulator. This consolidated modulator may be tested todetermine if it has a higher binding affinity for the target than eitherof the two individual modulators. A consolidated modulator is selectedas a modulator when it has a higher binding affinity for the target thaneither of the two modulators. Larger consolidated modulators can beconstructed in an analogous manner, e.g., linking three modulators whichbind to three nearby regions on the target to form a multilinkedconsolidated modulator that has an even higher affinity for the targetthan the linked modulator. In this example, it is assumed that isdesirable to have the modulator bind to all the druggable regions.However, it may be the case that binding to certain of the druggableregions is not desirable, so that the same techniques may be used toidentify modulators and consolidated modulators that show increasedspecificity based on binding to at least one but not all druggableregions of a target.

The present invention provides a number of methods that use drug designas described above. For example, in one aspect, the present inventioncontemplates a method for designing a candidate compound for screeningfor inhibitors of a polypeptide of the invention, the method comprising:(a) determining the three dimensional structure of a crystallizedpolypeptide of the invention or a fragment thereof; and (b) designing acandidate inhibitor based on the three dimensional structure of thecrystallized polypeptide or fragment.

In another aspect, the present invention contemplates a method foridentifying a potential inhibitor of a polypeptide of the invention, themethod comprising: (a) providing the three-dimensional coordinates of apolypeptide of the invention or a fragment thereof; (b) identifying adruggable region of the polypeptide or fragment; and (c) selecting froma database at least one compound that comprises three dimensionalcoordinates which indicate that the compound may bind the druggableregion; (d) wherein the selected compound is a potential inhibitor of apolypeptide of the invention.

In another aspect, the present invention contemplates a method foridentifying a potential modulator of a molecule comprising a druggableregion similar to that of SEQ ID NO: 2 or SEQ ID NO: 4, the methodcomprising: (a) using the atomic coordinates of amino acid residues fromSEQ ID NO: 2 or SEQ ID NO: 4, or a fragment thereof, +a root mean squaredeviation from the backbone atoms of the amino acids of not more than1.5 Å, to generate a three-dimensional structure of a moleculecomprising a druggable region that is a portion of SEQ ID NO: 2 or SEQID NO: 4; (b) employing the three dimensional structure to design orselect the potential modulator; (c) synthesizing the modulator; and (d)contacting the modulator with the molecule to determine the ability ofthe modulator to interact with the molecule.

In another aspect, the present invention contemplates an apparatus fordetermining whether a compound is a potential inhibitor of a polypeptidehaving SEQ ID NO: 2 or SEQ ID NO: 4, the apparatus comprising: (a) amemory that comprises: (i) the three dimensional coordinates andidentities of the atoms of a polypeptide of the invention or a fragmentthereof that form a druggable site; and (ii) executable instructions;and (b) a processor that is capable of executing instructions to: (i)receive three-dimensional structural information for a candidatecompound; (ii) determine if the three-dimensional structure of thecandidate compound is complementary to the structure of the interior ofthe druggable site; and (iii) output the results of the determination.

In another aspect, the present invention contemplates a method fordesigning a potential compound for the prevention or treatment of E.faecalis related disease or disorder, the method comprising: (a)providing the three dimensional structure of a crystallized polypeptideof the invention, or a fragment thereof; (b) synthesizing a potentialcompound for the prevention or treatment of E. faecalis related diseaseor disorder based on the three dimensional structure of the crystallizedpolypeptide or fragment; (c) contacting a polypeptide of the presentinvention or an E. faecalis with the potential compound; and (d)assaying the activity of a polypeptide of the present invention, whereina change in the activity of the polypeptide indicates that the compoundmay be useful for prevention or treatment of a E. faecalis relateddisease or disorder.

In another aspect, the present invention contemplates a method fordesigning a potential compound for the prevention or treatment of E.faecalis related disease or disorder, the method comprising: (a)providing structural information of a druggable region derived from NMRspectroscopy of a polypeptide of the invention, or a fragment thereof;(b) synthesizing a potential compound for the prevention or treatment ofE. faecalis related disease or disorder based on the structuralinformation; (c) contacting a polypeptide of the present invention or anE. faecalis with the potential compound; and (d) assaying the activityof a polypeptide of the present invention, wherein a change in theactivity of the polypeptide indicates that the compound may be usefulfor prevention or treatment of a E. faecalis related disease ordisorder.

(b) In Vitro Assays

Polypeptides of the invention may be used to assess the activity ofsmall molecules and other modulators in in vitro assays. In oneembodiment of such an assay, agents are identified which modulate thebiological activity of a protein, protein-protein interaction ofinterest or protein complex, such as an enzymatic activity, binding toother cellular components, cellular compartmentalization, signaltransduction, and the like. In certain embodiments, the test agent is asmall organic molecule.

Assays may employ kinetic or thermodynamic methodology using a widevariety of techniques including, but not limited to, microcalorimetry,circular dichroism, capillary zone electrophoresis, nuclear magneticresonance spectroscopy, fluorescence spectroscopy, and combinationsthereof.

The invention also provides a method of screening compounds to identifythose which modulate the action of polypeptides of the invention, orpolynucleotides encoding the same. The method of screening may involvehigh-throughput techniques. For example, to screen for modulators, asynthetic reaction mix, a cellular compartment, such as a membrane, cellenvelope or cell wall, or a preparation of any thereof, comprising apolypeptide of the invention and a labeled substrate or ligand of suchpolypeptide is incubated in the absence or the presence of a candidatemolecule that may be a modulator of a polypeptide of the invention. Theability of the candidate molecule to modulate a polypeptide of theinvention is reflected in decreased binding of the labeled ligand ordecreased production of product from such substrate. Detection of therate or level of production of product from substrate may be enhanced byusing a reporter system. Reporter systems that may be useful in thisregard include but are not limited to calorimetric labeled substrateconverted into product, a reporter gene that is responsive to changes ina nucleic acid of the invention or polypeptide activity, and bindingassays known in the art.

Another example of an assay for a modulator of a polypeptide of theinvention is a competitive assay that combines a polypeptide of theinvention and a potential modulator with molecules that bind to apolypeptide of the invention, recombinant molecules that bind to apolypeptide of the invention, natural substrates or ligands, orsubstrate or ligand mimetics, under appropriate conditions for acompetitive inhibition assay. Polypeptides of the invention can belabeled, such as by radioactivity or a calorimetric compound, such thatthe number of molecules of a polypeptide of the invention bound to abinding molecule or converted to product can be determined accurately toassess the effectiveness of the potential modulator.

A number of methods for identifying a molecule which modulates theactivity of a polypeptide are known in the art. For example, in one suchmethod, a subject polypeptide is contacted with a test compound, and theactivity of the subject polypeptide in the presence of the test compoundis determined, wherein a change in the activity of the subjectpolypeptide is indicative that the test compound modulates the activityof the subject polypeptide. In certain instances, the test compoundagonizes the activity of the subject polypeptide, and in otherinstances, the test compound antagonizes the activity of the subjectpolypeptide.

In another example, a compound which modulates SEQ ID NO: 2 or SEQ IDNO: 4 dependent growth or infectivity of E. faecalis may be identifiedby (a) contacting a polypeptide of the invention with a test compound;and (b) determining the activity of the polypeptide in the presence ofthe test compound, wherein a change in the activity of the polypeptideis indicative that the test compound may modulate the growth orinfectivity of E. faecalis.

(c) In Vivo Assays

Animal models of bacterial infection and/or disease may be used as an invivo assay for evaluating the effectiveness of a potential drug targetin treating or preventing diseases or disorders. A number of suitableanimal models are described briefly below, however, these models areonly examples and modifications, or completely different animal models,may be used in accord with the methods of the invention.

(i) Mouse Soft Tissue Model

The mouse soft tissue infection model is a sensitive and effectivemethod for measurement of bacterial proliferation. In these models(Vogelman et al., 1988, J. Infect. Dis. 157: 287-298) anesthetized miceare infected with the bacteria in the muscle of the hind thigh. The micecan be either chemically immune compromised (e.g., cytoxan treated at125 mg/kg on days −4, −2, and 0) or immunocompetent. The dose of microbenecessary to cause an infection is variable and depends on theindividual microbe, but commonly is on the order of 10⁵-10⁶ colonyforming units per injection for bacteria. A variety of mouse strains areuseful in this model although Swiss Webster and DBA2 lines are mostcommonly used. Once infected the animals are conscious and show no overtill effects of the infections for approximately 12 hours. After thattime virulent strains cause swelling of the thigh muscle, and theanimals can become bacteremic within approximately 24 hours. This modelmost effectively measures proliferation of the microbe, and thisproliferation is measured by sacrifice of the infected animal andcounting colonies from homogenized thighs.

(ii) Diffusion Chamber Model

A second model useful for assessing the virulence of microbes is thediffusion chamber model (Malouin et al., 1990, Infect. Immun. 58:1247-1253; Doy et al., 1980, J. Infect. Dis. 2: 39-51; Kelly et al.,1989, Infect. Immun. 57: 344-350. In this model rodents have a diffusionchamber surgically placed in the peritoneal cavity. The chamber consistsof a polypropylene cylinder with semipermeable membranes covering thechamber ends. Diffusion of peritoneal fluid into and out of the chamberprovides nutrients for the microbes. The progression of the “infection”may be followed by examining growth, the exoproduct production or RNAmessages. The time experiments are done by sampling multiple chambers.

(iii) Endocarditis Model

For bacteria, an important animal model effective in assessingpathogenicity and virulence is the endocarditis model (J. Santoro and M.E. Levinson, 1978, Infect. Immun. 19: 915-918). A rat endocarditis modelcan be used to assess colonization, virulence and proliferation.

(iv) Osteomyelitis Model

A fourth model useful in the evaluation of pathogenesis is theosteomyelitis model (Spagnolo et al., 1993, Infect. Immun. 61:5225-5230). Rabbits are used for these experiments. Anesthetized animalshave a small segment of the tibia removed and microorganisms aremicroinjected into the wound. The excised bone segment is replaced andthe progression of the disease is monitored. Clinical signs,particularly inflammation and swelling are monitored. Termination of theexperiment allows histolic and pathologic examination of the infectionsite to complement the assessment procedure.

(v) Murine Septic Arthritis Model

A fifth model relevant to the study of microbial pathogenesis is amurine septic arthritis model (Abdelnour et al., 1993, Infect. Immun.61: 3879-3885). In this model mice are infected intravenously andpathogenic organisms are found to cause inflammation in distal limbjoints. Monitoring of the inflammation and comparison of inflammationvs. inocula allows assessment of the virulence of related strains.

(vi) Bacterial Peritonitis Model

Finally, bacterial peritonitis offers rapid and predictive data on thevirulence of strains (M. G. Bergeron, 1978, Scand. J. Infect. Dis.Suppl. 14: 189-206; S. D. Davis, 1975, Antimicrob. Agents Chemother. 8:50-53). Peritonitis in rodents, such as mice, can provide essential dataon the importance of targets. The end point may be lethality or clinicalsigns can be monitored. Variation in infection dose in comparison tooutcome allows evaluation of the virulence of individual strains.

A variety of other in vivo models are available and may be used whenappropriate for specific pathogens or specific test agents. For example,target organ recovery assays (Gordee et al., 1984, J. Antibiotics37:1054-1065; Bannatyne et al., 1992, Infect. 20:168-170) may be usefulfor fungi and for bacterial pathogens which are not acutely virulent toanimals.

It is also relevant to note that the species of animal used for aninfection model, and the specific genetic make-up of that animal, maycontribute to the effective evaluation of the effects of a particulartest agent. For example, immuno-incompetent animals may, in someinstances, be preferable to immuno-competent animals. For example, theaction of a competent immune system may, to some degree, mask theeffects of the test agent as compared to a similar infection in animmuno-incompetent animal. In addition, many opportunistic infections,in fact, occur in immuno-compromised patients, so modeling an infectionin a similar immunological environment is appropriate.

10. Vaccines

There are provided by the invention, products, compositions and methodsfor raising immunological response against a pathogen, especially E.faecalis. In one aspect, a polypeptide of the invention or a nucleicacid of the invention, or an antigenic fragment thereof, may beadministered to a subject, optionally with a booster, adjuvant, or othercomposition that stimulates immune responses.

Another aspect of the invention relates to a method for inducing animmunological response in an individual, particularly a mammal whichcomprises inoculating the individual with a polypeptide of the inventionand/or a nucleic acid of the invention, adequate to produce antibodyand/or T cell immune response to protect said individual from infection,particularly bacterial infection and most particularly E. faecalisinfection. Also provided are methods whereby such immunological responseslows bacterial replication. Yet another aspect of the invention relatesto a method of inducing immunological response in an individual whichcomprises delivering to such individual a nucleic acid vector, sequenceor ribozyme to direct expression of a polypeptide of the inventionand/or a nucleic acid of the invention in vivo in order to induce animmunological response, such as, to produce antibody and/or T cellimmune response, including, for example, cytokine-producing T cells orcytotoxic T cells, to protect said individual, preferably a human, fromdisease, whether that disease is already established within theindividual or not. One example of administering the gene is byaccelerating it into the desired cells as a coating on particles orotherwise. Such nucleic acid vector may comprise DNA, RNA, a ribozyme, amodified nucleic acid, a DNA/RNA hybrid, a DNA-protein complex or anRNA-protein complex.

A further aspect of the invention relates to an immunologicalcomposition that when introduced into an individual, preferably a human,capable of having induced within it an immunological response, inducesan immunological response in such individual to a nucleic acid of theinvention and/or a polypeptide encoded therefrom, wherein thecomposition comprises a recombinant nucleic acid of the invention and/orpolypeptide encoded therefrom and/or comprises DNA and/or RNA whichencodes and expresses an antigen of said nucleic acid of the invention,polypeptide encoded therefrom, or other polypeptide of the invention.The immunological response may be used therapeutically orprophylactically and may take the form of antibody immunity and/orcellular immunity, such as cellular immunity arising from CTL or CD4+ Tcells.

In another embodiment, the invention relates to compositions comprisinga polypeptide of the invention and an adjuvant. The adjuvant can be anyvehicle which would typically enhance the antigenicity of a polypeptide,e.g., minerals (for instance, alum, aluminum hydroxide or aluminumphosphate), saponins complexed to membrane protein antigens (immunestimulating complexes), pluronic polymers with mineral oil, killedmycobacteria in mineral oil, Freund's complete adjuvant, bacterialproducts, such as muramyl dipeptide (MDP) and lipopolysaccharide (LPS),as well as lipid A, liposomes, or any of the other adjuvants known inthe art. A polypeptide of the invention can be emulsified with, absorbedonto, or coupled with the adjuvant.

A polypeptide of the invention may be fused with co-protein or chemicalmoiety which may or may not by itself produce antibodies, but which iscapable of stabilizing the first protein and producing a fused ormodified protein which will have antigenic and/or immunogenicproperties, and preferably protective properties. Thus fused recombinantprotein, may further comprise an antigenic co-protein, such aslipoprotein D from Hemophilus influenzae, Glutathione-S-transferase(GST) or beta-galactosidase, or any other relatively large co-proteinwhich solubilizes the protein and facilitates production andpurification thereof. Moreover, the co-protein may act as an adjuvant inthe sense of providing a generalized stimulation of the immune system ofthe organism receiving the protein. The co-protein may be attached toeither the amino- or carboxy-terminus of a polypeptide of the invention.

Provided by this invention are compositions, particularly vaccinecompositions, and methods comprising the polypeptides and/orpolynucleotides of the invention and immunostimulatory DNA sequences,such as those described in Sato, Y. et al. Science 273: 352 (1996).

Also, provided by this invention are methods using the describedpolynucleotide or particular fragments thereof, which have been shown toencode non-variable regions of bacterial cell surface proteins, inpolynucleotide constructs used in such genetic immunization experimentsin animal models of infection with E. faecalis. Such experiments will beparticularly useful for identifying protein epitopes able to provoke aprophylactic or therapeutic immune response. It is believed that thisapproach will allow for the subsequent preparation of monoclonalantibodies of particular value, derived from the requisite organ of theanimal successfully resisting or clearing infection, for the developmentof prophylactic agents or therapeutic treatments of bacterial infection,particularly E. faecalis infection, in mammals, particularly humans.

A polypeptide of the invention may be used as an antigen for vaccinationof a host to produce specific antibodies which protect against invasionof bacteria, for example by blocking adherence of bacteria to damagedtissue.

11. Array Analysis

In part, the present invention is directed to the use of subject nucleicacids in arrays to assess gene expression. In another part, the presentinvention is directed to the use of subject nucleic acids in arrays forE. faecalis. In yet another part, the present invention contemplatesusing the subject nucleic acids to interact with probes contained onarrays.

In one aspect, the present invention contemplates an array comprising asubstrate having a plurality of addresses, wherein at least one of theaddresses has disposed thereon a capture probe that can specificallybind to a nucleic acid of the invention. In another aspect, the presentinvention contemplates a method for detecting expression of a nucleotidesequence which encodes a polypeptide of the invention, or a fragmentthereof, using the foregoing array by: (a) providing a sample comprisingat least one mRNA molecule; (b) exposing the sample to the array underconditions which promote hybridization between the capture probedisposed on the array and a nucleic acid complementary thereto; and (c)detecting hybridization between an mRNA molecule of the sample and thecapture probe disposed on the array, thereby detecting expression of asequence which encodes for a polypeptide of the invention, or a fragmentthereof.

Arrays are often divided into microarrays and macroarrays, wheremicroarrays have a much higher density of individual probe species perarea. Microarrays may have as many as 1000 or more different probes in a1 cm² area. There is no concrete cut-off to demarcate the differencebetween micro- and macroarrays, and both types of arrays arecontemplated for use with the invention.

Microarrays are known in the art and generally consist of a surface towhich probes that correspond in sequence to gene products (e.g., cDNAs,mRNAs, oligonucleotides) are bound at known positions. In oneembodiment, the microarray is an array (e.g., a matrix) in which eachposition represents a discrete binding site for a product encoded by agene (e.g., a protein or RNA), and in which binding sites are presentfor products of most or almost all of the genes in the organism'sgenome. In certain embodiments, the binding site or site is a nucleicacid or nucleic acid analogue to which a particular cognate cDNA canspecifically hybridize. The nucleic acid or analogue of the binding sitemay be, e.g., a synthetic oligomer, a full-length cDNA, a less-than fulllength cDNA, or a gene fragment.

Although in certain embodiments the microarray contains binding sitesfor products of all or almost all genes in the target organism's genome,such comprehensiveness is not necessarily required. Usually themicroarray will have binding sites corresponding to at least 100, 500,1000, 4000 genes or more. In certain embodiments, arrays will haveanywhere from about 50, 60, 70, 80, 90, or even more than 95% of thegenes of a particular organism represented. The microarray typically hasbinding sites for genes relevant to testing and confirming a biologicalnetwork model of interest. Several exemplary human microarrays arepublicly available.

The probes to be affixed to the arrays are typically polynucleotides.These DNAs can be obtained by, e.g., polymerase chain reaction (PCR)amplification of gene segments from genomic DNA, cDNA (e.g., by RT-PCR),or cloned sequences. PCR primers are chosen, based on the known sequenceof the genes or cDNA, that result in amplification of unique fragments(e.g., fragments that do not share more than 10 bases of contiguousidentical sequence with any other fragment on the microarray). Computerprograms are useful in the design of primers with the requiredspecificity and optimal amplification properties. See, e.g., Oligo plversion 5.0 (National Biosciences). In an alternative embodiment, thebinding (hybridization) sites are made from plasmid or phage clones ofgenes, cDNAs (e.g., expressed sequence tags), or inserts therefrom(Nguyen et al., 1995, Genomics 29:207-209).

A number of methods are known in the art for affixing the nucleic acidsor analogues to a solid support that makes up the array (Schena et al.,1995, Science 270:467-470; DeRisi et al., 1996, Nature Genetics14:457-460; Shalon et al., 1996, Genome Res. 6:639-645; and Schena etal., 1995, Proc. Natl. Acad. Sci. USA 93:10539-11286).

Another method for making microarrays is by making high-densityoligonucleotide arrays (Fodor et al., 1991, Science 251:767-773; Peaseet al., 1994, Proc. Natl. Acad. Sci. USA 91:5022-5026; Lockhart et al.,1996, Nature Biotech 14:1675; U.S. Pat. Nos. 5,578,832; 5,556,752; and5,510,270; Blanchard et al., 1996, 11: 687-90).

Other methods for making microarrays, e.g., by masking (Maskos andSouthern, 1992, Nuc. Acids Res. 20:1679-1684), may also be used. Inprincipal, any type of array, for example, dot blots on a nylonhybridization membrane (see Sambrook et al., Molecular Cloning—ALaboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y., 1989), could be used, although, as will berecognized by those of skill in the art.

The nucleic acids to be contacted with the microarray may be prepared ina variety of ways, and may include nucleotides of the subject invention.Such nucleic acids are often labeled fluorescently. Nucleic acidhybridization and wash conditions are chosen so that the population oflabeled nucleic acids will specifically hybridize to appropriate,complementary nucleic acids affixed to the matrix. Non-specific bindingof the labeled nucleic acids to the array can be decreased by treatingthe array with a large quantity of non-specific DNA—a so-called“blocking” step.

When fluorescently labeled probes are used, the fluorescence emissionsat each site of a transcript array may be detected by scanning confocallaser microscopy. When two fluorophores are used, a separate scan, usingthe appropriate excitation line, is carried out for each of the twofluorophores used. Fluorescent microarray scanners are commerciallyavailable from Affymetrix, Packard BioChip Technologies, BioRobotics andmany other suppliers. Signals are recorded, quantitated and analyzedusing a variety of computer software.

According to the method of the invention, the relative abundance of anmRNA in two cells or cell lines is scored as a perturbation and itsmagnitude determined (i.e., the abundance is different in the twosources of mRNA tested), or as not perturbed (i.e., the relativeabundance is the same). As used herein, a difference between the twosources of RNA of at least a factor of about 25% (RNA from one source is25% more abundant in one source than the other source), more usuallyabout 50%, even more often by a factor of about 2 (twice as abundant), 3(three times as abundant) or 5 (five times as abundant) is scored as aperturbation. Present detection methods allow reliable detection ofdifference of an order of about 2-fold to about 5-fold, but moresensitive methods are expected to be developed.

In addition to identifying a perturbation as positive or negative, it isadvantageous to determine the magnitude of the perturbation. This can becarried out, as noted above, by calculating the ratio of the emission ofthe two fluorophores used for differential labeling, or by analogousmethods that will be readily apparent to those of skill in the art.

In certain embodiments, the data obtained from such experiments reflectsthe relative expression of each gene represented in the microarray.Expression levels in different samples and conditions may now becompared using a variety of statistical methods.

12. Pharmaceutical Compositions

Pharmaceutical compositions of this invention include any modulatoridentified according to the present invention, or a pharmaceuticallyacceptable salt thereof, and a pharmaceutically acceptable carrier,adjuvant, or vehicle. The term “pharmaceutically acceptable carrier”refers to a carrier(s) that is “acceptable” in the sense of beingcompatible with the other ingredients of a composition and notdeleterious to the recipient thereof.

Methods of making and using such pharmaceutical compositions are alsoincluded in the invention. The pharmaceutical compositions of theinvention can be administered orally, parenterally, by inhalation spray,topically, rectally, nasally, buccally, vaginally, or via an implantedreservoir. The term parenteral as used herein includes subcutaneous,intracutaneous, intravenous, intramuscular, intra articular,intrasynovial, intrasternal, intrathecal, intralesional, andintracranial injection or infusion techniques.

Dosage levels of between about 0.01 and about 100 mg/kg body weight perday, preferably between about 0.5 and about 75 mg/kg body weight per dayof the modulators described herein are useful for the prevention andtreatment of disease and conditions, including E. faecalis mediateddiseases and conditions. The amount of active ingredient that may becombined with the carrier materials to produce a single dosage form willvary depending upon the host treated and the particular mode ofadministration. A typical preparation will contain from about 5% toabout 95% active compound (w/w). Alternatively, such preparationscontain from about 20% to about 80% active compound.

13. Antimicrobial Agents

The polypeptides of the invention may be used to develop antimicrobialagents for use in a wide variety of applications. The uses are as variedas surface disinfectants, topical pharmaceuticals, personal hygieneapplications (e.g., antimicrobial soap, deodorant or the like),additives to cell culture medium, and systemic pharmaceutical products.Antimicrobial agents of the invention may be incorporated into a widevariety of products and used to treat an already existing microbialinfection/contamination or may be used prophylactically to suppressfuture infection/contamination.

The antimicrobial agents of the invention may be administered to a site,or potential site, of infection/contamination in either a liquid orsolid form. Alternatively, the agent may be applied as a coating to asurface of an object where microbial growth is undesirable usingnonspecific absorption or covalent attachment. For example, implants ordevices (such as linens, cloth, plastics, heart pacemakers, surgicalstents, catheters, gastric tubes, endotracheal tubes, prostheticdevices) can be coated with the antimicrobials to minimize adherence orpersistence of bacteria during storage and use. The antimicrobials mayalso be incorporated into such devices to provide slow release of theagent locally for several weeks during healing. The antimicrobial agentsmay also be used in association with devices such as ventilators, waterreservoirs, air-conditioning units, filters, paints, or othersubstances. Antimicrobials of the invention may also be given orally orsystemically after transplantation, bone replacement, during dentalprocedures, or during implantation to prevent colonization withbacteria.

In another embodiment, antimicrobial agents of the invention may be usedas a food preservative or in treating food products to eliminatepotential pathogens. The latter use might be targeted to the fish andpoultry industries that have serious problems with enteric pathogenswhich cause severe human disease. In a further embodiment, the agents ofthe invention may be used as antimicrobials for food crops, either asagents to reduce post harvest spoilage or to enhance host resistance.The antimicrobials may also be used as preservatives in processed foodseither alone or in combination with antibacterial food additives such aslysozymes.

In another embodiment, the antimicrobials of the invention may be usedas an additive to culture medium to prevent or eliminate infection ofcultured cells with a pathogen.

14. OTHER EMBODIMENTS

In addition to other embodiments, aspects and objects of the presentinvention disclosed herein, including the claims appended hereto, thefollowing paragraphs set forth additional, non-limiting embodiments andother aspects of the present invention (with all references toparagraphs contained in this section referring to other aspect of thepresent invention (with all references to paragraphs contained in thissections referring to other paragraphs set forth in this sections):

1. A composition comprising an isolated, recombinant polypeptide,wherein the polypeptide comprises: (a) an amino acid sequence set forthin SEQ ID NO: 2 or SEQ ID NO: 4; (b) an amino acid sequence having atleast about 95% identity with the amino acid sequence set forth in SEQID NO: 2 or SEQ ID NO: 4; or (c) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis; and wherein the polypeptide of (a), (b) or (c) is at leastabout 90% pure in a sample of the composition.

2. The composition of paragraph 1, wherein the polypeptide is at leastabout 95% pure as determined by gel electrophoresis.

3. The composition of paragraph 1, wherein the polypeptide is purifiedto essential homogeneity.

4. The composition of paragraph 1, wherein at least about two-thirds ofthe polypeptide in the sample is soluble.

5. The composition of paragraph 1, wherein the polypeptide is fused toat least one heterologous polypeptide that increases the solubility orstability of the polypeptide.

6. The composition of paragraph 1, which further comprises a matrixsuitable for mass spectrometry.

7. The composition of paragraph 5, wherein the matrix is a nicotinicacid derivative or a cinnamic acid derivative.

8. A sample comprising an isolated, recombinant polypeptide, wherein thepolypeptide comprises: (a) an amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4; (b) an amino acid sequence having at least about95% identity with the amino acid sequence set forth in SEQ ID NO: 2 orSEQ ID NO: 4; or (c) an amino acid sequence encoded by a polynucleotidethat hybridizes under stringent conditions to the complementary strandof a polynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at leastone biological activity of guanylate kinase from E. faecalis; andwherein the polypeptide of (a), (b) or (c) is labeled with a heavy atom.

9. The sample of paragraph 8 wherein the heavy atom is one of thefollowing: cobalt, selenium, krypton, bromine, strontium, molybdenum,ruthenium, rhodium, palladium, silver, cadmium, tin, iodine, xenon,barium, lanthanum, cerium, praseodymium, neodymium, samarium, europium,gadolinium, terbium, dysprosium, holmium, erbium, thulium, ytterbium,lutetium, tantalum, tungsten, rhenium, osmium, iridium, platinum, gold,mercury, thallium, lead, thorium and uranium.

10. The sample of paragraph 9, wherein the polypeptide is labeled withseleno-methionine.

11. The sample of paragraph 8, further comprising a cryo-protectant.

12. The sample of paragraph 11, wherein the cryo-protectant is one ofthe following: methyl pentanediol, isopropanol, ethylene glycol,glycerol, formate, citrate, mineral oil and a low-molecular-weightpolyethylene glycol.

13. A crystallized, recombinant polypeptide comprising: (a) an aminoacid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (b) an aminoacid sequence having at least about 95% identity with the amino acidsequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (c) an amino acidsequence encoded by a polynucleotide that hybridizes under stringentconditions to the complementary strand of a polynucleotide having SEQ IDNO: 1 or SEQ ID NO: 3 and has at least one biological activity ofguanylate kinase from E. faecalis; wherein the polypeptide of (a), (b)or (c) is in crystal form.

14. A crystallized complex comprising the crystallized, recombinantpolypeptide of paragraph 11 and a co-factor, wherein the complex is incrystal form.

15. A crystallized complex comprising the crystallized, recombinantpolypeptide of paragraph 11 and a small organic molecule, wherein thecomplex is in crystal form.

16. The crystallized, recombinant polypeptide of paragraph 11, whichdiffracts x-rays to a resolution of about 3.5 Å or better.

17. The crystallized, recombinant polypeptide of paragraph 11, whereinthe polypeptide comprises at least one heavy atom label.

18. The crystallized, recombinant polypeptide of paragraph 17, whereinthe polypeptide is labeled with seleno-methionine.

19. A method for designing a modulator for the prevention or treatmentof E. faecalis related disease or disorder, comprising:

(a) providing a three-dimensional structure for a crystallized,recombinant polypeptide of paragraph 11;

(b) identifying a potential modulator for the prevention or treatment ofE. faecalis related disease or disorder by reference to thethree-dimensional structure;

(c) contacting a polypeptide of the composition of paragraph 1 or E.faecalis with the potential modulator; and

(d) assaying the activity of the polypeptide or determining theviability of E. faecalis after contact with the modulator, wherein achange in the activity of the polypeptide or the viability of E.faecalis indicates that the modulator may be useful for prevention ortreatment of a E. faecalis related disease or disorder.

20. A sample comprising an isolated, recombinant polypeptide, whereinthe polypeptide comprises: (a) an amino acid sequence set forth in SEQID NO: 2 or SEQ ID NO: 4; (b) an amino acid sequence having at leastabout 95% identity with the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO: 4; or (c) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis; and wherein the polypeptide of (a), (b) or (c) is enrichedin at least one NMR isotope.

21. The sample of paragraph 20, wherein the NMR isotope is one of thefollowing: hydrogen-1 (¹H), hydrogen-2 (²H), hydrogen-3 (³H),phosphorous-31 (³¹P), sodium-23 (²³Na), nitrogen-14 (¹⁴N), nitrogen-15(¹⁵N), carbon-13 (¹³C) and fluorine-19 (¹⁹F).

22. The sample of paragraph 20, further comprising a deuterium locksolvent.

23. The sample of paragraph 22, wherein the deuterium lock solvent isone of the following: acetone (CD₃COCD₃), chloroform (CDCl₃), dichloromethane (CD₂Cl₂), methylnitrile (CD₃CN), benzene (C₆D₆), water (D₂O),diethylether ((CD₃CD₂)₂O), dimethylether ((CD₃)₂O),N,N-dimethylformamide ((CD₃)₂NCDO), dimethyl sulfoxide (CD₃SOCD₃),ethanol (CD₃CD₂OD), methanol (CD₃OD), tetrahydrofuran (C₄D₈O), toluene(C₆D₅CD₃), pyridine (C₅DsN) and cyclohexane (C₆H₁₂).

24. The sample of paragraph 20, which is contained within an NMR tube.

25. A method for identifying small molecules that bind to a polypeptideof the composition of paragraph 1, comprising:

(a) generating a first NMR spectrum of an isotopically labeledpolypeptide of the composition of paragraph 1;

(b) exposing the polypeptide to one or more small molecules;

(c) generating a second NMR spectrum of the polypeptide which has beenexposed to one or more small molecules; and

(d) comparing the first and second spectra to determine differencesbetween the first and the second spectra, wherein the differences areindicative of one or more small molecules that have bound to thepolypeptide.

26. A host cell comprising a nucleic acid encoding a polypeptidecomprising: (a) an amino acid sequence set forth in SEQ ID NO: 2 or SEQID NO: 4; (b) an amino acid sequence having at least about 95% identitywith the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4;or (c) an amino acid sequence encoded by a polynucleotide thathybridizes under stringent conditions to the complementary strand of apolynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at least onebiological activity of guanylate kinase from E. faecalis; wherein aculture of the host cell produces at least about 1 mg of the polypeptideper liter of culture and the polypeptide is at least about one-thirdsoluble as measured by gel electrophoresis.

27. An isolated, recombinant polypeptide, comprising: (a) an amino acidsequence having at least about 90% identity with the amino acid sequenceset forth in SEQ ID NO: 4; or (b) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis; and wherein the polypeptide comprises one or more of thefollowing amino acid residues at the specified position of thepolypeptide: K20, T21, A22, R135, R131, 1168, S35, R40, R43, Y52, E71,Y80, V82, A99, T101, and R145.

28. A method for obtaining structural information of a crystallizedpolypeptide, the method comprising:

(a) crystallizing a recombinant polypeptide, wherein the polypeptidecomprises: (1) an amino acid sequence set forth in SEQ ID NO: 2 or SEQID NO: 4; (2) an amino acid sequence having at least about 95% identitywith the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4;or (3) an amino acid sequence encoded by a polynucleotide thathybridizes under stringent conditions to the complementary strand of apolynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at least onebiological activity of guanylate kinase from E. faecalis; and whereinthe crystallized polypeptide is capable of diffracting X-rays to aresolution of 3.5 Å or better; and

(b) analyzing the crystallized polypeptide by X-ray diffraction todetermine the three-dimensional structure of at least a portion of thecrystallized polypeptide.

29. The method of paragraph 28, wherein the three-dimensional structureof the portion of the crystallized polypeptide is determined to aresolution of 3.5 Å or better.

30. A method for identifying a druggable region of a polypeptide, themethod comprising:

(a) obtaining crystals of a polypeptide comprising (1) an amino acidsequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) an amino acidsequence having at least about 95% identity with the amino acid sequenceset forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (3) an amino acid sequenceencoded by a polynucleotide that hybridizes under stringent conditionsto the complementary strand of a polynucleotide having SEQ ID NO: 1 orSEQ ID NO: 3 and has at least one biological activity of guanylatekinase from E. faecalis, such that the three dimensional structure ofthe crystallized polypeptide may be determined to a resolution of 3.5 Åor better;

(b) determining the three dimensional structure of the crystallizedpolypeptide using X-ray diffraction; and

(c) identifying a druggable region of the crystallized polypeptide basedon the three-dimensional structure of the crystallized polypeptide.

31. The method of paragraph 30, wherein the druggable region is anactive site.

32. The method of paragraph 30, wherein the druggable region is on thesurface of the polypeptide.

33. Crystalline guanylate kinase from E. faecalis comprising a crystalhaving unit cell dimensions a=57.908 Å, b=57.908 Å, c=138.424 Å, a==y=90°, with space group P4₃2₁2 and one molecule per asymmetric unit.

34. A crystallized polypeptide comprising (1) an amino acid sequence setforth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) an amino acid sequence havingat least about 95% identity with the amino acid sequence set forth inSEQ ID NO: 2 or SEQ ID NO: 4; or (3) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis; wherein the crystal has a P4₃2₁2 space group.

35. A crystallized polypeptide comprising a structure of a polypeptidethat is defined by a substantial portion of the atomic coordinates setforth in FIG. 12.

36. A method for determining the crystal structure of a homolog of apolypeptide, the method comprising:

(a) providing the three dimensional structure of a first crystallizedpolypeptide comprising (1) an amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4; (2) an amino acid sequence having at least about95% identity with the amino acid sequence set forth in SEQ ID NO: 2 orSEQ ID NO: 4; or (3) an amino acid sequence encoded by a polynucleotidethat hybridizes under stringent conditions to the complementary strandof a polynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at leastone biological activity of guanylate kinase from E. faecalis;

(b) obtaining crystals of a second polypeptide comprising an amino acidsequence that is at least 70% identical to the amino acid sequence setforth in SEQ ID NO: 2 or SEQ ID NO: 4, such that the three dimensionalstructure of the second crystallized polypeptide may be determined to aresolution of 3.5 Å or better; and

(c) determining the three dimensional structure of the secondcrystallized polypeptide by x-ray crystallography based on the atomiccoordinates of the three dimensional structure provided in step (a).

37. The method of paragraph 36, wherein the atomic coordinates for thesecond crystallized polypeptide have a root mean square deviation fromthe backbone atoms of the first polypeptide of not more than 1.5 Å forall backbone atoms shared in common with the first polypeptide and thesecond polypeptide.

38. A method for homology modeling a homolog of guanylate kinase from E.faecalis, comprising:

(a) aligning the amino acid sequence of a homolog of guanylate kinasefrom E. faecalis with an amino acid sequence of SEQ ID NO: 2 or SEQ IDNO: 4 and incorporating the sequence of the homolog of guanylate kinasefrom E. faecalis into a model of guanylate kinase from E. faecalisderived from structure coordinates as listed in FIG. 12 to yield apreliminary model of the homolog of guanylate kinase from E. faecalis;

(b) subjecting the preliminary model to energy minimization to yield anenergy minimized model;

(c) remodeling regions of the energy minimized model wherestereochemistry restraints are violated to yield a final model of thehomolog of guanylate kinase from E. faecalis.

39. A method for obtaining structural information about a molecule or amolecular complex of unknown structure comprising:

(a) crystallizing the molecule or molecular complex;

(b) generating an x-ray diffraction pattern from the crystallizedmolecule or molecular complex;

(c) applying at least a portion of the structure coordinates set forthin FIG. 12 to the x-ray diffraction pattern to generate athree-dimensional electron density map of at least a portion of themolecule or molecular complex whose structure is unknown.

40. A method for attempting to make a crystallized complex comprising apolypeptide and a modulator having a molecular weight of less than 5kDa, the method comprising:

(a) crystallizing a polypeptide comprising (1) an amino acid sequenceset forth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) an amino acid sequencehaving at least about 95% identity with the amino acid sequence setforth in SEQ ID NO: 2 or SEQ ID NO: 4; or (3) an amino acid sequenceencoded by a polynucleotide that hybridizes under stringent conditionsto the complementary strand of a polynucleotide having SEQ ID NO: 1 orSEQ ID NO: 3 and has at least one biological activity of guanylatekinase from E. faecalis; such that crystals of the crystallizedpolypeptide will diffract x-rays to a resolution of 5 Å or better; and

(b) soaking the crystals in a solution comprising a potential modulatorhaving a molecular weight of less than 5 kDa.

41. A method for incorporating a potential modulator in a crystal of apolypeptide, comprising placing a crystal of guanylate kinase from E.faecalis having unit cell dimensions a=57.908 Å, b=57.908 Å, c=138.424Å, a ===90=, with space group P4₃2₁2, in a solution comprising thepotential modulator.

42. A computer readable storage medium comprising digitally encodedstructural data, wherein the data comprises structural coordinates aslisted in FIG. 12 for the backbone atoms of at least about six aminoacid residues from a druggable region of guanylate kinase from E.faecalis.

43. A scalable three-dimensional configuration of points, at least aportion of the points derived from some or all of the structurecoordinates as listed in FIG. 12 for a plurality of amino acid residuesfrom a druggable region of guanylate kinase from E. faecalis.

44. The scalable three-dimensional configuration of points of paragraph43, wherein the structure coordinates as listed in FIG. 12 for thebackbone atoms of at least about five amino acid residues from adruggable region of guanylate kinase from E. faecalis are used to derivepart or all of the portion of points.

45. The scalable three-dimensional configuration of points of paragraph43, wherein the structure coordinates as listed in FIG. 12 for thebackbone and optionally the side chain atoms of at least about ten aminoacid residues from a druggable region of guanylate kinase from E.faecalis are used to derive part or all of the portion of points.

46. The scalable three-dimensional configuration of points of paragraph43, wherein the structure coordinates as listed in FIG. 12 for thebackbone atoms of at least about fifteen amino acid residues from adruggable region of guanylate kinase from E. faecalis are used to derivepart or all of the portion of points.

47. The scalable three-dimensional configuration of points of paragraph43, wherein substantially all of the points are derived from structurecoordinates as listed in FIG. 12.

48. The scalable three-dimensional configuration of points of paragraph43, wherein the structure coordinates as listed in FIG. 12 for the atomsof the amino acid residues from any of the above-described druggableregions of guanylate kinase from E. faecalis are used to derive part orall of the portion of points:

49. A scalable three-dimensional configuration of points, comprisingpoints having a root mean square deviation of less than about 1.5 Å fromthe three dimensional coordinates as listed in FIG. 12 for the backboneatoms of at least five amino acid residues, wherein the five amino acidresidues are from a druggable region of guanylate kinase from E.faecalis.

50. The scalable three-dimensional configuration of points of paragraph49, wherein any point-to-point distance, calculated from the threedimensional coordinates as listed in FIG. 12, between one of thebackbone atoms for one of the five amino acid residues and anotherbackbone atom of a different one of the five amino acid residues is notmore than about 10 Å.

51. A scalable three-dimensional configuration of points comprisingpoints having a root mean square deviation of less than about 1.5 Å fromthe three dimensional coordinates as listed in FIG. 12 for the atoms ofthe amino acid residues from any of the above-described druggableregions of guanylate kinase from E. faecalis:

52. A computer readable storage medium comprising digitally encodedstructural data, wherein the data comprise the identity andthree-dimensional coordinates as listed in FIG. 12 for the atoms of theamino acid residues from any of the above-described druggable regions ofguanylate kinase from E. faecalis:

53. A scalable three-dimensional configuration of points, wherein thepoints have a root mean square deviation of less than about 1.5 Å fromthe three dimensional coordinates as listed in FIG. 12 for the atoms ofthe amino acid residues from any of the above-described druggableregions of guanylate kinase from E. faecalis, wherein up to one aminoacid residue in each of the regions may have a conservative substitutionthereof.

54. A scalable three-dimensional configuration of points derived from adruggable region of a polypeptide, wherein the points have a root meansquare deviation of less than about 1.5 Å from the three dimensionalcoordinates as listed in FIG. 12 for the backbone atoms of at least tenamino acid residues that participate in the intersubunit contacts ofguanylate kinase from E. faecalis.

55. A computer-assisted method for identifying an inhibitor of theactivity of guanylate kinase from E. faecalis, comprising:

(a) supplying a computer modeling application with a set of structurecoordinates as listed in FIG. 12 for the atoms of the amino acidresidues from any of the above-described druggable regions of guanylatekinase from E. faecalis so as to define part or all of a molecule orcomplex;

(b) supplying the computer modeling application with a set of structurecoordinates of a chemical entity; and

(c) determining whether the chemical entity is expected to bind to orinterfere with the molecule or complex.

56. The method of paragraph 55, wherein determining whether the chemicalentity is expected to bind to or interfere with the molecule or complexcomprises performing a fitting operation between the chemical entity anda druggable region of the molecule or complex, followed bycomputationally analyzing the results of the fitting operation toquantify the association between the chemical entity and the druggableregion.

57. The method of paragraph 55, further comprising screening a libraryof chemical entities.

58. A computer-assisted method for designing an inhibitor of guanylatekinase activity comprising:

(a) supplying a computer modeling application with a set of structurecoordinates having a root mean square deviation of less than about 1.5 Åfrom the structure coordinates as listed in FIG. 12 for the atoms of theamino acid residues from any of the above-described druggable regions ofguanylate kinase from E. faecalis so as to define part or all of amolecule or complex;

(b) supplying the computer modeling application with a set of structurecoordinates for a chemical entity;

(c) evaluating the potential binding interactions between the chemicalentity and the molecule or complex;

(d) structurally modifying the chemical entity to yield a set ofstructure coordinates for a modified chemical entity; and

(e) determining whether the modified chemical entity is an inhibitorexpected to bind to or interfere with the molecule or complex, whereinbinding to or interfering with the molecule or molecular complex isindicative of potential inhibition of guanylate kinase activity.

59. The method of paragraph 58, wherein determining whether the modifiedchemical entity is an inhibitor expected to bind to or interfere withthe molecule or complex comprises performing a fitting operation betweenthe chemical entity and the molecule or complex, followed bycomputationally analyzing the results of the fitting operation toevaluate the association between the chemical entity and the molecule orcomplex.

60. The method of paragraph 58, wherein the set of structure coordinatesfor the chemical entity is obtained from a chemical library.

61. A computer-assisted method for designing an inhibitor of guanylatekinase activity de novo comprising:

(a) supplying a computer modeling application with a set ofthree-dimensional coordinates derived from the structure coordinates aslisted in FIG. 12 for the atoms of the amino acid residues from any ofthe above-described druggable regions of guanylate kinase from E.faecalis so as to define part or all of a molecule or complex;

(b) computationally building a chemical entity represented by a set ofstructure coordinates; and

(c) determining whether the chemical entity is an inhibitor expected tobind to or interfere with the molecule or complex, wherein binding to orinterfering with the molecule or complex is indicative of potentialinhibition of guanylate kinase activity.

62. The method of paragraph 61, wherein determining whether the chemicalentity is an inhibitor expected to bind to or interfere with themolecule or complex comprises performing a fitting operation between thechemical entity and a druggable region of the molecule or complex,followed by computationally analyzing the results of the fittingoperation to quantify the association between the chemical entity andthe druggable region.

63. The method of any of paragraphs 55, 58 or 61, further comprisingsupplying or synthesizing the potential inhibitor, then assaying thepotential inhibitor to determine whether it inhibits guanylate kinaseactivity.

64. A method for identifying a potential modulator for the prevention ortreatment of a E. faecalis related disease or disorder, the methodcomprising:

(a) providing the three dimensional structure of a crystallizedpolypeptide comprising: (1) an amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4; (2) an amino acid sequence having at least about95% identity with the amino acid sequence set forth in SEQ ID NO: 2 orSEQ ID NO: 4; or (3) an amino acid sequence encoded by a polynucleotidethat hybridizes under stringent conditions to the complementary strandof a polynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at leastone biological activity of guanylate kinase from E. faecalis;

(b) obtaining a potential modulator for the prevention or treatment ofE. faecalis related disease or disorder based on the three dimensionalstructure of the crystallized polypeptide;

(c) contacting the potential modulator with a second polypeptidecomprising: (i) an amino acid sequence set forth in SEQ ID NO: 2 or SEQID NO: 4; (ii) an amino acid sequence having at least about 95% identitywith the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4;or (iii) an amino acid sequence encoded by a polynucleotide thathybridizes under stringent conditions to the complementary strand of apolynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at least onebiological activity of guanylate kinase from E. faecalis; which secondpolypeptide may optionally be the same as the crystallized polypeptide;and

(d) assaying the activity of the second polypeptide, wherein a change inthe activity of the second polypeptide indicates that the compound maybe useful for prevention or treatment of a E. faecalis related diseaseor disorder.

65. A method for designing a candidate modulator for screening forinhibitors of a polypeptide, the method comprising:

(a) providing the three dimensional structure of a druggable region of apolypeptide comprising (1) an amino acid sequence set forth in SEQ IDNO: 2 or SEQ ID NO: 4; (2) an amino acid sequence having at least about95% identity with the amino acid sequence set forth in SEQ ID NO: 2 orSEQ ID NO: 4; or (3) an amino acid sequence encoded by a polynucleotidethat hybridizes under stringent conditions to the complementary strandof a polynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at leastone biological activity of guanylate kinase from E. faecalis; and

(b) designing a candidate modulator based on the three dimensionalstructure of the druggable region of the polypeptide.

66. A method for identifying a potential modulator of a polypeptide froma database, the method comprising:

(a) providing the three-dimensional coordinates for a plurality of theamino acids of a polypeptide comprising (1) an amino acid sequence setforth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) an amino acid sequence havingat least about 95% identity with the amino acid sequence set forth inSEQ ID NO: 2 or SEQ ID NO: 4; or (3) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis;

(b) identifying a druggable region of the polypeptide; and

(c) selecting from a database at least one potential modulatorcomprising three dimensional coordinates which indicate that themodulator may bind or interfere with the druggable region.

67. The method of paragraph 66, wherein the modulator is a smallmolecule.

68. A method for preparing a potential modulator of a druggable regioncontained in a polypeptide, the method comprising:

(a) using the atomic coordinates for the backbone atoms of at leastabout six amino acid residues from a polypeptide of SEQ ID NO: 4, with a± a root mean square deviation from the backbone atoms of the amino acidresidues of not more than 1.5 Å, to generate one or morethree-dimensional structures of a molecule comprising a druggable regionfrom the polypeptide;

(b) employing one or more of the three dimensional structures of themolecule to design or select a potential modulator of the druggableregion; and

(c) synthesizing or obtaining the modulator.

69. An apparatus for determining whether a compound is a potentialmodulator of a polypeptide, the apparatus comprising:

(a) a memory that comprises:

(i) the three dimensional coordinates and identities of at least aboutfifteen atoms from a druggable region of a polypeptide comprising (1) anamino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) anamino acid sequence having at least about 95% identity with the aminoacid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (3) an aminoacid sequence encoded by a polynucleotide that hybridizes understringent conditions to the complementary strand of a polynucleotidehaving SEQ ID NO: 1 or SEQ ID NO: 3 and has at least one biologicalactivity of guanylate kinase from E. faecalis;

(ii) executable instructions; and

(b) a processor that is capable of executing instructions to:

(i) receive three-dimensional structural information for a candidatemodulator;

(ii) determine if the three-dimensional structure of the candidatemodulator is complementary to the three dimensional coordinates of theatoms from the druggable region; and

(iii) output the results of the determination.

70. A method for making an inhibitor of guanylate kinase activity, themethod comprising chemically or enzymatically synthesizing a chemicalentity to yield an inhibitor of guanylate kinase activity, the chemicalentity having been identified during a computer-assisted processcomprising supplying a computer modeling application with a set ofstructure coordinates of a molecule or complex, the molecule or complexcomprising at least a portion of at least one druggable region fromguanylate kinase from E. faecalis; supplying the computer modelingapplication with a set of structure coordinates of a chemical entity;and determining whether the chemical entity is expected to bind or tointerfere with the molecule or complex at a druggable region, whereinbinding to or interfering with the molecule or complex is indicative ofpotential inhibition of guanylate kinase activity.

71. A computer readable storage medium comprising digitally encodeddata, wherein the data comprises structural coordinates for a druggableregion that is structurally homologous to the structure coordinates aslisted in FIG. 12 for a druggable region of guanylate kinase from E.faecalis.

72. A computer readable storage medium comprising digitally encodedstructural data, wherein the data comprise a majority of thethree-dimensional structure coordinates as listed in FIG. 12.

73. The computer readable storage medium of paragraph 72, furthercomprising the identity of the atoms for the majority of thethree-dimensional structure coordinates as listed in FIG. 12.

74. The computer readable storage medium of paragraph 72, wherein thedata comprise substantially all of the three-dimensional structurecoordinates as listed in FIG. 12.

EXEMPLIFICATION

The invention now being generally described, it will be more readilyunderstood by reference to the following examples which are includedmerely for purposes of illustration of certain aspects and embodimentsof the present invention, and are not intended to limit the invention inany way.

Example 1 Isolation and Cloning of Nucleic Acid

Enterococcus faecalis is a facultative Gram-positive anaerobe bacteriathat is associated with both community and hospital acquired infections.Approximately 80% of enteroccocal infections in humans are caused by E.faecalis. The most common enterococcal-associated nosocomial infectionsare infections of the urinary tract, followed by surgical woundinfections and bacteremia. Other enterococcal infections include intraabdominal and pelvic infections, central nervous system infections, andin rare instances, osteomyelitis and pulmonary infections. The highvirulence of the organism and the ability of many strains to resistnumerous anti-microbial agents, presents difficult therapeutic issues.Most enterococci are relatively resistant to penicillin, ampicillin, andthe ureidopenicillins. E. faecalis polynucleotide sequences wereobtained from The Institute of Genomic Research (TIGR) (Rockville, Md.;www.tigr.org). E. faecalis genomic DNA is extracted from a crushed cellpellet (strain V583) and and subjected to 10% sucrose and 2% SDS in a60° C. water bath, followed by the addition of 1 M NaCl for a 40 minuteincubation on ice. Impurities, including RNA and proteins, are removedby enzymatic degradation via RNAse and phenol-chloroform extractions,respectively. The DNA is then precipitated, washed with ethanol, andquantified by UV absorption.

The coding sequences of the subject nucleic acid sequences (predicted)are obtained by reference to either publicly available databases or fromthe use of a bioinformatics program that is used to select the codingsequence of interest from the applicable genome. For example,bioinformatics programs that may be used to select the coding sequenceof interest from the genome of E. faecalis include that described inNucleic Acids Research, 1999, 27:4636-4641 and the ContigExpress andTranslate functionalities of Vector NTI Suite (InforMax).

The coding DNA is amplified from purified genomic DNA using PCR withprimers that are identified with a computer program. The PCR primers areselected so as to introduce restriction enzyme cleavage sites at theflanking regions of the DNA (e.g., Nde1 and BglII). The forward andreverse primers have SEQ ID NO: 5 and SEQ ID NO: 6. The sequences of theprimers are shown in FIG. 5, and their respective restriction sites andmelting temperatures are shown in Table 1 of FIG. 6.

The PCR reaction is performed using 50-100 ng of chromosomal DNA and 2Units of a high fidelity DNA Polymerase (for example Pfu Turbo(Stratagene) or Platinum Pfx (Invitrogen)). The thermocycling conditionsfor the PCR process include a DNA melting step at 94° C. for 45 sec, aprimer annealing step at 48° C.-58° C. (depending on Primer [Tm]) for 45sec, and an extension step at 68° C.-72° C. (depending on enzyme) for 1min 45 sec-2 min 30 sec (depending on size of DNA). After 25-30 cycles,a final blocking step at 72° C. for 9 min is carried out.

The amplified nucleic acid product is isolated from the PCR cocktailusing silica-gel membrane based column chromatography (Qiagen). Thequality of the PCR product is assessed by resolving an aliquot ofamplified product on a 1% agarose gel. The DNA is quantifiedspectrophotometrically at A₂₆₀ or by visualizing the resolved genes witha 302 nm UV-B light source.

The PCR product is directionally cloned into the polylinker region ofany of three expression vectors: pET28 (Novagen), pET15 (Novagen) orpGEX (Pharmacia/LKB Biotechnology). Additional restriction enzyme sitesmay be engineered into the expressions vectors to allow for simultaneousclones to be prepared having different purification tags. After theligation reaction, the DNA is transformed into competent E. coli cells(Strains XL1-Blue (Stratagene) or DH5α (Invitrogen)) via heat shock orelectroporation as described in Sambrook, et al., Molecular Cloning: ALaboratory Manual, 2^(nd) Ed., Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y. (1989). The expression vectors contain thebacteriophage T7 promoter for RNA polymerase, and the E. coli strainused produces T7 RNA polymerase upon induction withisopropyl-β-D-thiogalactoside (IPTG). The sequence of the cloning siteadds a Glutathione S-transferase (GST) tag, or a polyhistidine (6×His)tag, at the N- or C-terminus of the recombinant protein. The cloningsite also inserts a cleavage site for the thrombin or Tev (Invitrogen)enzymes between the recombinant protein and the N- or C-terminal GST orpolyhistidine tag.

Transformants are selected using the appropriate antibiotic (Ampicillinor Kanamycin) and identified using PCR, or another method, to analyzetheir DNA. The polynucleotide sequence cloned into the expressionconstruct is then isolated using a modified alkaline lysis method(Birnboim, H. C., and Doly, J. (1979) Nucl. Acids Res. 7, 1513-1522.)The sequence of the clone is verified by standard polynucleotidesequencing methods. The published nucleic acid and amino acid sequencesare presented in FIG. 1 and FIG. 2. The experimentally determinednucleic acid sequence is presented in FIG. 3, and the amino acidsequence predicted from the sequence of FIG. 3 is presented in FIG. 4.

The expression construct is transformed into a bacterial host strainBL21-Gold (DE3) supplemented with a plasmid called pUBS520, whichdirects expression of tRNA for arginine (agg and aga) and serves toaugment the expression of the recombinant protein in the host cell(Gene, vol. 85 (1989) 109-114). The expression construct may also betransformed into BL21-Gold (DE3) without pUBS520, BL21-Gold (DE3)Codon-Plus (RIL) or (RP) (Stratagene) or Roseatta (DE3) (Novagen), thelatter two of which contain genes encoding tRNAs. Alternatively, theexpression construct may be transformed into BL21 STAR E. coli(Invitrogen) cells which has an Rnase deficiency that reducesdegradation of recombinant mRNA transcript and therefore increases theprotein yield. The recombinant protein is then assayed for positiveoverexpression in the host and the presence of the protein in thecytoplasmic (water soluble) region of the cell.

Example 2 Test Protein Expression and Solubility

(a) Test Expression

Transformed cells are grown in LB medium supplemented with theappropriate antibiotics up to a final concentration of 100 μg/ml. Thecultures are shaken at 37° C. until they reach an optical density(OD₆₀₀) between 0.6 and 0.7. The cultures are then induced withisopropyl-beta-D-thiogalactopyranoside (IPTG) to a final concentrationof 0.5 mM at 15° C. for 10 hours, 25° C. for 4 hours, or 30° C. for 4hours.

(b) Method One for Determining Protein Solubility Levels

The cells are harvested by centrifugation and subjected to a freeze/thawcycle. The cells are lysed using detergent, sonication, or incubationwith lysozyme. Total and soluble proteins are assayed using a 26-wellBioRad Criterion gel running system. The proteins are stained with anappropriate dye (Coomassie, Silver stain, or Sypro-Red) and visualizedwith the appropriate visualization system. Typically, recombinantprotein is seen as a prominent band in the lanes of the gel representingthe soluble fraction.

(c) Method Two for Determining Protein Solubility Levels

The soluble and insoluble fractions (in the presence of 6M urea) of thecell pellet are bound to the appropriate affinity column. The purifiedproteins from both fractions are analysed by SDS-PAGE and the levels ofprotein in the soluble fraction are determined.

The approximate percent solubility of the polypeptide having thesequence of SEQ ID NO: 4 is determined using one of the foregoingmethods, and the resulting percent solubility is presented in Table 1 ofFIG. 6.

Example 3 Native Protein Expression

The expression construct clone encoding the soluble polypeptide havingthe amino acid sequence of SEQ ID NO: 4 is introduced into an expressionhost. The resultant cell line is then grown in culture. The method ofgrowth is dependant on whether the protein to be purified is a nativeprotein or a labeled protein. For native and ¹⁵N labeled proteinproduction, a Gold-pUBS520 (as described above), BL21-Gold (DE3)Codon-Plus (RIL) or (RP), or BL21 STAR E. Coli cell line is used. Forgenerating proteins metabolically labeled with selenium, the clone isintroduced into a strain called B834 (Novagen). The methods forexpressing labeled polypeptides of the invention are described in theExamples that follow.

In one method for expressing an unlabeled polypeptide of the invention,2L LB cultures or 1L TB cultures are inoculated with a 1% (v/v) starterculture (OD₆₀₀ of 0.8). The cultures are shaken at 37° C. and 200 rpmand grown to an OD₆₀₀ of 0.6-0.8 followed by induction with 0.5 mM IPTGat 15° C. and 200 rpm for at least 10 hours or at 25° C. for 4 hours.

The cells are harvested by centrifugation and the pellets areresuspended in 25 ml HEPES buffer (50 mM, pH 7.5), supplemented with 100μl of protease inhibitors (PMSF and benzamidine (Sigma)) andflash-frozen in liquid nitrogen.

Alternatively, for an unlabeled polypeptide of the invention, a starterculture is prepared in a 300 mL Tunair flask (Shelton Scientific) byadding 20 mL of medium having 47.6 g/L of Terrific Broth and 1.5%glycerol in dH₂O followed by autoclaving for 30 minutes at 121° C. and15 psi. When the broth cools to room temperature, the medium issupplemented with 6.3 μM CoCl₂-6H₂O, 33.2 μM MnSO₄.5H₂O, 5.9 μMCuCl₂-2H₂O, 8.1 μM H₃BO₃, 8.3 μM Na₂MoO₄.2H₂O, 7 μM ZnSO₄.7H₂O, 108 μMFeSO₄.7H₂O, 68 μM CaCl₂-2H₂O, 4.1 μM AlCl₃-6H₂O, 8.4 μM NiCl₂-6H₂O, 1 mMMgSO₄, 0.5% v/v of Kao and Michayluk vitamins mix (Sigma; Cat. No.K3129), 25 μg/mL Carbenicillin, and 50 μg/mL Kanamycin. The medium isthen inoculated with several colonies of the freshly transformedexpression construct of interest. The culture is incubated at 37° C. and260 rpm for about 3 hours and then transferred to a 2.5 L Tunair Flaskcontaining 1 L of the above media. The 1 L culture is then incubated at37° C. with shaking at 230-250 rpm on an orbital shaker having a 1 inchorbital diameter. When the culture reaches an OD₆₀₀ of 3-6 it is inducedwith 0.5 mM IPTG. The induced culture is then incubated at 15° C. withshaking at 230-250 rpm or faster for about 6-15 hours. The cells areharvested by centrifugation at 3500 rpm at 4° C. for 20 minutes and thecell pellet is resuspended in 15 mL ice cold binding buffer (Hepes 50mM, pH 7.5) and 100 μl of protease inhibitors (50 mM PMSF and 100 mMBenzamidine, stock concentration) and flash frozen.

Example 4 Expression of Selmet Labeled Polypeptides

The freshly transformed cell, harboring a plasmid with a nucleic acidencoding a polypeptide of the invention, is inoculated into 20 ml of NMM(New Minimal Medium) and shaken at 37° C. for 8-9 hours. This culture isthen transferred into a 6 L Erlenmeyer flask containing 2 L of minimummedium (M9). The media is supplemented with all amino acids exceptmethionine. All amino acids are added as a solution except for Tyrosine,Tryptophan and Phenylalanine which are added to the media in powderformat. As well the media is supplemented with MgSO₄ (2 mM finalconcentration), FeSO₄.7H₂O (25 mg/L final concentration), Glucose (0.4%final concentration), CaCl₂ (0.1 mM final concentration) andSeleno-L-Methionine (40 mg/L final concentration). When the OD₆₀₀ of thecell culture reaches 0.8-0.9, IPTG (0.4 mM final concentration) is addedto the medium for protein induction, and the cell culture is keptshaking at 15° C. for 10 hours. The cells are harvested bycentrifugation at 3500 rpm at 4° C. for 20 minutes and the cell pelletis resuspended in 15 mL cold binding buffer (Hepes 50 mM, pH 7.5) and100 μl of protease inhibitors (PMSF and Benzamidine) and flash frozen.

Alternatively, a starter culture is prepared in a 300 mL Tunair flask(Shelton Scientific) by adding 50 mL of sterile medium having 10% 10×M9(37.4 mM NH₄Cl (Sigma; Cat. No. A4514), 44 mM KH₂PO₄ (Bioshop, Ontario,Canada; Cat. No. PPM 302), 96 mM Na₂HPO₄ (Sigma; Cat. No. S2429256), and96 mM Na₂HPO₄.7H₂O (Sigma; Cat. No. S9390) final concentration), 450 μMalanine, 190 μM arginine, 302 μM asparagine, 300 μM aspartic acid, 330μM cysteine, 272 μM glutamic acid, 274 μM glutamine, 533 μM glycine, 191μM histidine, 305 μM isoleucine, 305 μM leucine, 220 μM lysine, 242 μMphenylalanine, 348 μM proline, 380 μM serine, 336 μM threonine, 196 μMtryptophan, 220 μM tyrosine, and 342 μM valine, 204 μMSeleno-L-Methionine (Sigma; Cat. No. S3132), 0.5% v/v of Kao andMichayluk vitamins mix (Sigma; Cat. No. K3129), 2 mM MgSO₄ (Sigma; Cat.No. M7774), 90 μM FeSO₄.7H₂O (Sigma; Cat. No. F8633), 0.4% glucose(Sigma; Cat. No. G-5400), 100 μM CaCl₂ (Bioshop, Ontario, Canada; Cat.No. CCL 302), 50 μg/mL Ampicillin, and 50 μg/mL Kanamycin in dH₂O. Themedium is then inoculated with several colonies of E. coli B834 cells(Novagen) freshly transformed with an expression construct cloneencoding the polypeptide of interest. The culture is then incubated at37° C. and 200 rpm until it reaches an OD₆₀₀ of 1 and is thentransferred to a 2.5 L Tunair Flask containing 1 L of the above media.The 1 L culture is incubated at 37° C. with shaking at 200 rpm until theculture reaches an OD₆₀₀ of 0.6-0.8 and is then induced with 0.5 mMIPTG. The induced culture is incubated overnight at 15° C. with shakingat 200 rpm. The cells are harvested by centrifugation at 4200 rpm at 4°C. for 20 minutes and the cell pellet is resuspended in 15 mL ice coldbinding buffer (Hepes 50 mM, pH 7.5) and 100 μl of protease inhibitors(50 mM PMSF and 100 mM Benzamidine, stock concentration) and flashfrozen.

Alternatively, the cell harboring a plasmid with a nucleic acid encodinga polypeptide of the invention is inoculated into 10 ml of M9 minimummedium and kept shaking at 37° C. for 8-9 hours. This culture is thentransferred into a 2 L Baffled Flask (Corning) containing 1 L minimummedium. The media is supplemented with all amino acids exceptmethionine. All are added as a solution, except for Phenylalanine,Alanine, Valine, Leucine, Isoleucine, Proline, and Tryptophan which areadded to the media in powder format. As well the media is supplementedwith MgSO₄ (2 mM final concentrtion), FeSO₄.7H₂O (25 mg/L finalconcentration), Glucose (0.5% final concentration), CaCl₂ (0.1 mM finalconcentration) and Seleno-Methionine (50 mg/L final concentration). Whenthe OD₆₀₀ of the cell culture reaches 0.8-0.9, IPTG (0.8 mM finalconcentration) is added to the medium for protein induction, and thecell culture is kept shaking at 25° C. for 4 hours. The cells areharvested by centrifuged at 3500 rpm at 4° C. for 20 minutes and thecell pellet is resuspended in 10 mL cold binding buffer (Hepes 50 mM, pH7.5) and 100 μl of protease inhibitors (PMSF and Benzamidine) and flashfrozen.

Example 5 Expression of ¹⁵N Labeled Polypeptides

The cell, harboring a plasmid with a nucleic acid encoding a polypeptideof the invention, is inoculated into 2 L of minimal media (containing¹⁵N isotope, Cambridge Isotope Lab) in a 6 L Erlenmeyer flask. Theminimal media is supplemented with 0.01 mM ZnSO₄, 0.1 mM CaCl₂, 1 mMMgSO₄, 5 mg/L Thiamine.HCl, and 0.4% glucose. The 2 L culture is grownat 37° C. and 200 rpm to an OD₆₀₀ of between 0.7-0.8. The culture isthen induced with 0.5 mM IPTG and allowed to shake at 15° C. for 14hours. The cells are harvested by centrifugation and the cell pellet isresuspended in 15 mL cold binding buffer and 100 μl of proteaseinhibitor and flash frozen. The protein is then purified as describedbelow.

Alternatively, the freshly transformed cell, harboring a plasmid withthe gene of interest, is inoculated into 10 mL of M9 media (with ¹⁵Nisotope) and supplemented with with 0.01 mM ZnSO₄, 0.1 mM CaCl₂, 1 mMMgSO₄, 5 mg/L Thiamine.HCl, and 0.4% glucose. After 8-10 hours of growthat 37° C., the culture is transferred to a 2 L Baffled flask (Corning)containing 990 mL of the same media. When OD₆₀₀ of the culture isbetween 0.7-0.8, protein production is initiated by adding IPTG to afinal concentration of 0.8 mM and lowering the temperature to 25° C.After 4 hours of incubation at this temperature, the cells areharvested, and the cell pellet is resuspended in 10 mL cold bindingbuffer (Hepes 50 mM, pH 7.5) and 100 μl of protease inhibitor and flashfrozen.

Example 6 Method One for Purifying Polypeptides of the Invention

The frozen pellets are thawed and sonicated to lyse the cells (5×30seconds, output 4 to 5, 80% duty cycle, in a Branson Sonifier, VWR). Thelysates are clarified by centrifugation at 14,000 rpm for 60 min at 4°C. to remove insoluble cellular debris. The supernatants are removed andsupplemented with 1 μl of Benzonase Nuclease (25 U/μl, Novagen).

The recombinant protein is purified using DE52 (anion exchanger,Whatman) and Ni-NTA columns (Qiagen). The DE52 columns (30 mm wide,Biorad) are prepared by mixing 10 grams of DE52 resin in 25 ml of 2.5 MNaCl per protein sample, applying the resin to the column andequilibrating with 30 ml of binding buffer (50 mM in HEPES, pH 7.5, 5%glycerol (v/v), 0.5 M NaCl, 5 mM imidazole). Ni-NTA columns are preparedby adding 3.5-8 ml of resin to the column (20 mm wide, Biorad) based onthe level of expression of the recombinant protein and equilibrating thecolumn with 30 ml of binding buffer. The columns are arranged in tandemso that the protein sample is first passed over the DE52 column and thenloaded directly onto the Ni-NTA column.

The Ni-NTA columns are washed with at least 150 ml of wash buffer (50 mMHEPES, pH 7.5, 5% glycerol (v/v), 0.5 M NaCl, 30 mM imidazole) percolumn. A pump may be used to load and/or wash the columns. The proteinis eluted off of the Ni-NTA column using elution buffer (50 mM in HEPES,pH 7.5, 5% glycerol (v/v), 0.5 M NaCl, 250 mM imidazole) until no moreprotein is observed in the aliquots of eluate as measured using Bradfordreagent (Biorad). The eluate is supplemented with 1 mM of EDTA and 0.2mM DTT.

The samples are assayed by SDS-PAGE and stained with Coomassie Blue,with protein purity determined by visual staining.

Two methods may be used to remove the His tag located at either the C orN-terminus. In certain instances, the His tag may not be removed. Ineither case, the expressed polypeptide will have additional residuesattributable to the His tag, as shown in the following table: SEQ ID NOType of Tag and for Additional Whether or Not Residues AdditionalResidues Removed N/A GSH His tag removed from N-terminus SEQ ID NO: 7MGSSHHHHHHSSGLVPRGSH His tag not removed from N-terminus SEQ ID NO: 8GSENLYFQGHHHHHH His tag removed from C-terminus SEQ ID NO: 9 GSENLYFQHis tag not removed from C-terminus

In method one, a sample of purified polypeptide is supplemented with 2.5mM CaCl₂ and an appropriate amount of thrombin (the amount added willvary depending on the activity of the enzyme preparation) and incubatedfor ˜20-30 minutes on ice in order to remove the His tag. In method two,a sample of purified polypeptide is combined with thirty units ofrecombinant TEV protease in 50 mmol TRIS HCl pH=8.0, 0.5 mmol EDTA and 1mmol DTT, followed by incubation at 4° C. overnight, to remove the Histag.

The protein sample is then dialyzed in dialysis buffer (10 mM HEPES, pH7.5, 5% glycerol (v/v) and 0.5 M NaCl) for at least 8 hours using aSlide-A-Lyzer (Pierce) appropriate for the molecular weight of therecombinant protein. An aliquot of the cleaved and dialyzed samples isthen assayed by SDS-PAGE and stained with Coomassie Blue to determinethe purity of the protein and the success of cleavage.

The remainder of the sample is centrifuged at 2700 rpm at 4° C. for10-15 minutes to remove any precipitant and supplemented with 100 μl ofprotease inhibitor cocktail (0.1 M benzamidine and 0.05 M PMSF) (NOBioshop). The protein is then applied to a second Ni-NTA column (˜8 mlof resin) to remove the His-tags and eluted with binding buffer or washbuffer until no more protein is eluting off the column as assayed usingthe Bradford reagent. The eluted sample is supplemented with 1 mM EDTAand 0.6 mM of DTT and concentrated to a final volume of ˜15 mls using aMillipore Concentrator with an appropriately sized filter at 2700 rpm at4° C. The samples are then dialyzed overnight against crystallizationbuffer and concentrated to final volume of 0.3-0.7 ml.

Example 7 Method Two for Purifying Polypeptides of the Invention

The frozen pellets are thawed and supplemented with 100 μl of proteaseinhibitor (0.1 M benzamidine and 0.05 M PMSF), 0.5% CHAPS, and 4 U/mlBenzonase Nuclease. The sample is then gently rocked on a Nutator (VWR,setting 3) at room temperature for 30 minutes. The cells are then lysedby sonication (1×30 seconds, output 4 to 5, 80% duty cycle, in a BransonSonifier, VWR) and an aliquot is saved for a gel sample.

The recombinant protein is purified using a three column system. Thecolumns are set up in tandem so that the lysate flows from a BioradEcono (5.0×30 cm×589 ml) “lysate” column onto a Biorad Econo (2.5×20cm×98 ml) DE52 column and finally onto a Biorad Econo (1.5×15 cm×27 ml)Ni-NTA column. The lysate is mixed with 10 g of equilibrated DE52 resinand diluted to a total volume of 300 ml with binding buffer. Thismixture is poured into the first column which is empty. The remainder ofthe purification procedure is described in EXAMPLE 6 above.

Example 8 Method Three for Purifying Polypeptides of the Invention

The frozen pellets are thawed and sonicated to lyse the cells (5×30seconds, output 4 to 5, 80% duty cycle, in a Branson Sonifier, VWR). Thelysates are clarified by centrifugation at 14000 rpm for 60 min at 4° C.to remove insoluble cellular debris. The supernatants are removed andsupplemented with 1 μl of Benzonase Nuclease (25 U/μl, Novagen).

The recombinant protein is purified using DE52 (anion exchanger,Whatman) and Glutathione sepharose columns (Glutathione-Superflow resin,Clontech). The DE52 columns (30 mm wide, Biorad) are prepared by mixing10 grams of DE52 resin in 20 ml of 2.5 M NaCl per protein sample,applying the resin to the column and equilibrating with 30 ml of loadingbuffer (50 mM in HEPES, pH 7.5, 10% glycerol (v/v), 0.5 M NaCl, 1 mMEDTA, 1 mM DTT). Glutathione sepharose columns are prepared by adding 3ml of resin to the column (20 mm wide, Biorad) and equilibrating thecolumn with 30 ml of loading buffer. The columns are arranged in tandemso that the protein sample is first passed over the DE52 column and thenloads directly onto the Glutathione sepharose column.

The columns are washed with at least 150 ml of loading buffersupplemented with protease inhibitor cocktail (0.1 M benzamidine and0.05 M PMSF) per column. A pump may be used to load and/or wash thecolumns. The protein is eluted off of the Glutathione sepharose columnusing elution buffer (20 mM HEPES, pH 7.5, 0.5 M NaCl, 1 mM EDTA, 1 mMDTT; 25 mM glutathione (reduced form)) until no more protein is observedin the aliquots of eluate as measured using Biorad Bradford reagent.

The GST tag may be removed using thrombin or other procedures known inthe art. The protein samples are then dialyzed into crystallizationbuffer (10 mM Hepes, pH 7.5, 500 mM NaCl) to remove free glutathione andassayed by SDS-PAGE followed by staining with Coomassie blue. Prior touse or storage, the samples are concentrated to final volume of 0.3-0.5ml.

Using one or more of the methods described above, purified selmetlabeled polypeptide having SEQ ID NO: 4 is obtained in a yield ofapproximately 2.7 mg per liter of culture. The purified polypeptide isessentially the only protein visualized in the SDS-PAGE assay usingCoomassie Blue described above, which is at least about 95% or greaterpurity. The polypeptide so expressed and purified is His tagged (havingsequence GSENLYFQGHHHHHH) at the C-terminus as described above.

Using one or more of the methods described above, purified ¹⁵N labeledpolypeptide having SEQ ID NO: 4 is obtained in a yield of approximately3.1 mg per liter of culture. The purified polypeptide is essentially theonly protein visualized in the SDS-PAGE assay using Coomassie Bluedescribed above, which is at least about 95% or greater purity. Thepolypeptide so expressed and purified is His tagged (having sequenceMGSSHHHHHHSSGLVPRGSH) at the N-terminus.

The protein samples so prepared and purified may be used in thebiophysical studies that follow, with or without the His tag or theresidual amino acids resulting from removal of the His tag. In certaininstances, such as EXAMPLE 11, the polypeptide used may be a fusionprotein with a specific tag.

A stable solution of purified selmet labeled polypeptide having SEQ IDNO: 4, prepared and purified as described above, may be prepared with7.7 mg (or a lesser amount) of protein in one ml of either the dialysisor crystallization buffers (or possibly both) described above in EXAMPLE6 or EXAMPLE 8, respectively.

A stable solution of purified ¹⁵N labeled polypeptide having SEQ ID NO:4, prepared and purified as described above, may be prepared with 2.6 mg(or a lesser amount) of protein in one ml of either the dialysis orcrystallization buffers (or possibly both) described above in EXAMPLE 6or EXAMPLE 8, respectively.

Certain of the foregoing information is also set forth in Table 1 ofFIG. 6

Example 9 Mass Spectrometry Analysis Via Fingerprint Mapping

A gel slice from a purification protocol described above containing apolypeptide of the invention is cut into 1 mm cubes and 10 to 20 μl of1% acetic acid is added. After washing with 100-150 μl HPLC grade waterand removal of the liquid, acetonitrile (˜200 μl, approximately 3 to 4times the volume of the gel particles) is added followed by incubationat room temperature for 10 to 15 minutes with vortexing. A secondacetonitrile wash may be required to completely dehydrate the gelparticles. The protein in the gel particles is reduced at 50 degreesCelsius using 10 mM dithiothreitol (in 100 mM ammonium bicarbonate) andthen alkylated at room temperature in the dark using 55 mM iodoacetamide(in 100 mM ammonium bicarbonate). The gel particles are rinsed with aminimal volume of 100 mM ammonium bicarbonate before a trypsin (50 mMammonium bicarbonate, 5 mM CaCl₂, and 12.5 ng/μl trypsin) solution isadded. The gel particles are left on ice for 30 to 45 minutes (after 20minutes incubation more trypsin solution is added). The excess trypsinsolution is removed and 10 to 15 μl digestion buffer without trypsin isadded to ensure the gel particles remain hydrated during digestion.After digestion at 37° C., the supernatant is removed from the gelparticles. The peptides are extracted from the gel particles with 2changes of 100 μL of 100 mM ammonium bicarbonate with shaking for 45minutes and pooled with the initial gel supernatant. The extracts areacidified to 1% (v/v) with 100% acetic acid.

The tryptic peptides are purified with a C18 reverse phase resin. 250 μLof dry resin is washed twice with methanol and twice with 75%acetonitrile/1% acetic acid. A 5:1 slurry of solvent:resin is preparedwith 75% acetonitrile/1% acetic acid. To the extracted peptides, 2 μL ofthe resin slurry is added and the solution is shaken for 30 minutes atroom temperature. The supernatant is removed and replaced with 200 μL of2% acetonitrile/1% acetic acid and shaken for 5-15 minutes. Thesupernatant is removed and the peptides are eluted from the resin with15 μL of 75% acetonitrile/1% acetic acid with shaking for about 5minutes. The peptide and slurry mixture is applied to a filter plate andcentrifuged, and the filtrate is collected and stored at −70° C. untiluse.

Alternatively, the tryptic peptides are purified using ZipTip_(C18)(Millipore, Cat # ZTC18S960). The ZipTips are first pre-wetted byaspirating and dispensing 100% methanol. The tips are then washed with2% acetonitrile/1% acetic acid (5 times), followed by 65%acetonitrile/1% acetic (5 times) and returned to 2% acetonitrile/1%acetic acid (10 times). The digested peptides are bound to the ZipTipsby aspirating and dispensing the samples 5 times. Salts are removed bywashing ZipTips with 2% acetonitrile/1% acetic acid (5 times). 10 μL of65% acetonitrile/1% acetic acid is collected by the ZipTips anddispensed into a 96-well microtitre plate.

Analytical samples containing tryptic peptides are subjected toMALDI-TOF mass spectrometry. Samples are mixed 1:1 with a matrix ofα-cyano-4-hydroxy-trans-cinnamic acid. The sample/matrix mixture isspotted on to the MALDI sample plate with a robot, either a Gilson 215liquid handler or BioMek FX laboratory automation workstation (Beckman).The sample/matrix mixture is allowed to dry on the plate and is thenintroduced into the mass spectrometer. Analysis of the peptides in themass spectrometer is conducted using both delayed extraction mode (400ns delay) and an ion reflector to ensure high resolution of thepeptides.

Internally-calibrated tryptic peptide masses are searched againstdatabases using a correlative mass matching algorithm. The Proteometricssoftware package (ProteoMetrics) is utilized for batch databasesearching of tryptic peptide mass spectra. Statistical analysis isperformed on each protein match to determine its validity. Typicalsearch constraints include error tolerances within 0.1 Da formonoisotopic peptide masses, carboxyamidomethylation of cysteines, nooxidation of methionines allowed, and 0 or 1 missed enzyme cleavages.The software calculates the probability that a candidate in the databasesearch is the protein being analyzed, which is expressed as the Z-score.The Z-score is the distance to the population mean in unit of standarddeviation and corresponds to the percentile of the search in the randommatch population. If a search is in the 95th percentile, for example,about 5% of random matches could yield a higher Z-score than the search.A Z-score of 1.282 for a search indicates that the search is in the 90thpercentile, a Z-score of 1.645 indicates that the search is in the 95thpercentile, a Z-score of 2.326 indicates that the search is in the 99thpercentile, and a Z-score of 3.090 indicates that the search is in the99.9th percentile.

As shown in FIG. 9, and listed in Table 1 of FIG. 6, are the results ofthe mass search described above. The Z-score for the polypeptide of theinvention is 5.40E-05. The number of matched peptides for thepolypeptide of the invention is 11. The minimum sequence coverage forthe polypeptide of the invention is 70%. From this experiment, theidentity of the subject polypeptide has been confirmed.

Example 10 Mass Spectrometry Analysis Via High Mass

A matrix solution of 25 mg/mL of 3,5-dimethoxy-4-hydroxycinnamic acid(sinapinic acid) in 66% (v/v) a cetonitrile/1% (v/v) acetic acid isprepared along with an internal calibrant of carbonic anhydrase. On to astainless steel polished MALDI target, 1.5 μL of a protein solution(concentration of 2 μg/μL) is spotted, followed immediately by 1.5 μL ofmatrix. 3 μL of 40% (v/v) acetonitrile/1% (v/v) acetic acid is thenadded to each spot has dried. The sample is either spotted manually orutilizing a Gilson 215 liquid handler or BioMek FX laboratory automationworkstation (Beckman). The MALDI-TOF instrument utilizes positive ionand linear detection modes. Spectra are acquired automatically over amass to charge range from 0-150,000 Da, pulsed ion extraction delay isset at 200 ns, and 600 summed shots of 50-shot steps are completed.

The theoretical molecular weight of the protein for MALDI-TOF isdetermined from its amino acid sequence, taking into account anypurification tag or residue thereof still present and any labels (e.g.,selenomethionine or ¹⁵N). To account for ¹⁵N incorporation, an amountequal to the theoretical molecular weight of the protein divided by 70is added. The mass of water is subtracted from the overall molecularweight. The MALDI-TOF spectrum is calibrated with the internal calibrantof carbonic anhydrase (observed as either [MH⁺ _(avg)] 29025 or [MH₂ ²⁺]14513).

FIG. 10 displays a MALDI-TOF-generated mass spectrum of the intactpolypeptide of the present invention. The experimentally determinedmolecular weight of the polypeptide is listed in Table 1 of FIG. 6. Incertain instances, a lower mass to charge peak may also be present,which signifies the presence of doubly-charged molecular ion peak [MH₂²⁺] of the protein.

Example 11 Method One for Isolating and Identifying Interacting Proteins

(a) Method One for Preparation of Affinity Column

Micro-columns are prepared using forceps to bend the ends of P200pipette tips and adding 10 μl of glass beads to act as a column frit.Six micro-columns are required for every polypeptide to be studied. Themicro-columns are placed in a 96-well plate that has 1 mL wells. Next, aseries of solutions of the polypetide having SEQ ID NO: 4 or otherpolypeptide of the invention, prepared and purified as described aboveand with a GST tag on either terminus, is prepared so as to give finalamounts of 0, 0.1, 0.5, 1.0, and 2.0 mg of ligand per ml of resinvolume.

A slurry of Glutathione-Sepharose 4B (Amersham) is prepared and 0.5 mlslurry/ligand is removed (enough for six 40-μg aliquots of resin). Usinga glass frit Buchner funnel, the resin is washed sequentially with three10 ml portions each of distilled H₂O and 1 M ACB (20 mM HEPES pH 7.9, 1M NaCl, 10% glycerol, 1 mM DTT, and 1 mM EDTA). TheGlutathione-Sepharose 4B is completely drained of buffer, but not dried.The Glutathione-Sepharose 4B is resuspended as a 50% slurry in 1 M ACBand 80 μl is added to each micro-column to obtain 40 μg/column. Thebuffer containing the ligand concentration series is added to thecolumns and allowed to flow by gravity. The resin and ligand are allowedto cross-link overnight at 4° C. In the morning, micro-columns arewashed with 100 μl of 1 M ACB and allowed to flow by gravity. This isrepeated twice more and the elutions are tested for cross-linkingefficiency by measuring the amount of unbound ligand. After washing, themicro-columns are equilibrated using 200 μl of 0.1 M ACB (20 mM HEPES pH7.5, 0.1 M NaCl, 10% glycerol, 1 mM DTT, 1 mM EDTA).

In another method, the recombinant GST fusion protein can be replaced bya hexa-histidine fusion peptide for use with NTA-Agarose (Qiagen) as thesolid support. No adaptation to the above protocol is required for thesubstitution of NTA agarose for GST Sepharose except that therecombinant protein requires a six histidine fusion peptide in place ofthe GST fusion.

(b) Method Two for Preparation of Affinity Column

In an alternative method, GST-Sepharose 4B may be replaced by Affi-gel10 Gel (Bio-Rad). The column resin for affinity chromatography couldalso be Affigel 10 resin which allows for covalent attachment of theprotein ligand to the micro affinity column. An adaptation to the aboveprotocol for the use of this resin is a pre-wash of the resin with 100%isopropanol. No fusion peptides or proteins are required for the use ofAffigel 10 resin.

(c) Method One for Bacterial Extract Preparation

An E. faecalis extract is prepared from cell pellets using a Frenchpress followed by sonication. An E. faecalis cell pellet (˜6 g) issuspended in 3 pellet volumes (˜20 ml final volume) of 20 mM HEPES pH7.5, 150 mM NaCl, 10% glycerol, 10 mM MgSO₄, 10 mM CaCl₂, 1 mM DTT, 1 mMPMSF, 1 mM benzamidine, 40 μg/ml RNAse A, 75 units/ml S1 nuclease, and40 units/ml DNAse 1. The cell suspension is lysed with one pass with aFrench Pressure Cell followed by sonication on ice using three bursts of20 seconds each. The lysate is agitated at 4° C. for 30 minutes, broughtup to 0.5 M NaCl and then incubated for an additional 30 min at 4° C.with agitation. The lysate is centrifuged at 20,000 rpm for 1 hr in aJA25.50 Beckman rotor. The supernatant is removed and dialyzed overnightin a 3,500 Mr dialysis membrane against dialysis buffer (20 mM HEPES pH7.5, 10% glycerol, 1 mM DTT, 1 mM EDTA, 100 mM NaCl, 10 mM MgSO₄, 10 mMCaCl₂, 1 mM benzamidine, and 1 mM PMSF). The dialyzed protein extract isremoved from the dialysis tubing and frozen in one ml aliquots at −70°C.

(d) Method Two for Bacterial Extract Preparation

Bacterial cell extracts from E. faecalis are prepared from cell pelletsusing a Bead-Beater apparatus (Bio-spec Products Inc.) and zirconiabeads (0.1 mm diameter). The bacterial cell pellet is suspended (˜6 g)is suspended in 3 pellet volumes (˜20 ml final volume) of 20 mM HEPES pH7.5, 150 mM NaCl, 10% glycerol, 10 mM MgSO₄, 10 mM CaCl₂, 1 mM DTT, 1 mMPMSF, 1 mM benzamidine, 40 μg/ml RNAse A, 75 units/ml S1 nuclease, and40 units/ml DNAse 1. The cells are lysed with 10 pulses of 30 secbetween 90 sec pauses at a temperature of −5° C. The lysate is separatedfrom the zirconia beads using a standard column apparatus. The lysate iscentrifuged at 20000 rpm (48000×g) in a Beckman JA25.50 rotor. Thesupernatant is removed and dialyzed overnight at 4° C. against dialysisbuffer (20 mM HEPES pH 7.5, 10% glycerol, 1 mM DTT, 1 mM EDTA, 100 mMNaCl, 10 mM MgSO₄, 10 mM CaCl₂, 1 mM benzamidine, and 1 mM PMSF). Thedialyzed protein extract is removed from the dialysis tubing and frozenin one ml aliquots at −70° C.

(e) HeLa Cell Extract Preparation

A HeLa cell extract is prepared in the presence of protease inhibitors.Approximately 30 g of Hela cells are submitted to a freeze/thaw cycleand then divided into two tubes. To each tube 20 ml of Buffer A (10 mMHEPES pH 7.9, 1.5 mM MgCl, 10 mM KCl, 0.5 mM DTT, 0.5 mM PMSF) and aprotease inhibitor cocktail are added. The cell suspension ishomogenized with 10 strokes (2×5 strokes) to lyse the cells. Buffer B(15 ml per tube) is added (50 mM HEPES pH 7.9, 1.5 mM MgCl, 1.26 M NaCl,0.5 mM DTT, 0.5 mM PMSF, 0.5 mM EDTA, 75% glycerol) to each tubefollowed by a second round of homogenization (2×5 strokes). The lysatesare stirred on ice for 30 minutes followed by centrifugation 37,000 rpmfor 3 hr at 4° C. in a Ti70 fixed angle Beckman rotor. The supernatantis removed and dialyzed overnight in a 10,000 Mr dialysis membraneagainst dialysis buffer (20 mM HEPES pH 7.9, 10% glycerol, 1 mM DTT, 1mM EDTA, and 1 M NaCl. The dialyzed protein extract is removed from thedialysis tubing and frozen in one ml aliquots at −70° C.

(f) Affinity Chromatography

Cell extract is thawed and diluted to 5 mg/ml prior to loading 5 columnvolumes onto each micro-column. Each column is washed with 5 columnvolumes of 0.1 M ACB. This washing is repeated once. Each column is thenwashed with 5 column volumes of 0.1 M ACB containing 0.1% Triton X-100.The columns are eluted with 4 column volumes of 1% sodium dodecylsulfate into a 96 well PCR plate. To each eluted fraction is addedone-tenth volume of 10-fold concentrated loading buffer for SDS-PAGE.

(g) Resolution of the Eluted Proteins and Detection of Bound Proteins

The components of the eluted samples are resolved on SDS-polyacrylamidegels containing 13.8% polyacrylamide using the Laemmli buffer system andstained with silver nitrate. The bands containing the interactingprotein are excised with a clean scalpel. The gel volume is kept to aminimum by cutting as close to the band as possible. The gel slice isplaced into one well of a low protein binding, 96-well round-bottomplate. To the gel slices is added 20 μl of 1% acetic acid.

Example 12 Method Two for Isolating and Identifying Interacting Proteins

Interacting proteins may be isolated using immunoprecipitation.Naturally-occurring bacterial or eukaryotic cells are grown in definedgrowth conditions or the cells can be genetically manipulated with aprotein expression vector. The protein expression vector is used totransiently transfect the cDNA of interest into eukaryotic orprokaryotic cells and the protein is expressed for up to 24 or 48 hours.The cells are harvested and washed three times in sterile 20 mM HEPES(pH7.4)/Hanks balanced salts solution (H/H). The cells are finallyresuspended in culture media and incubated at 37° C. for 4-8 hr.

The harvested cells may be subjected to one or more culture conditionsthat may alter the protein profile of the cells for a given period oftime. The cells are collected and washed with ice-cold H/H that includes10 mM sodium pyrophosphate, 10 mM sodium fluoride, 10 mM EDTA, and 1 mMsodium orthovanadate. The cells are then lysed in lysis buffer (50 mMTris-HCl (pH 8.0), 150 mM NaCl, 1% Triton X-100, 10 mM sodiumpyrophosphate, 10 mM sodium fluoride, 10 mM EDTA, 1 mM sodiumorthovanadate, 1 μg/mL PMSF, 1 μg/mL aprotinin, 1 μg/mL leupeptin, and 1μg/mL pepstatin A) by gentle mixing, and placed on ice for 5 minutes.After lysis, the lysate is transferred to centrifuge tubes andcentrifuged in an ultracentrifuge at 75000 rpm for 15 min at 4° C. Thesupernatant is transferred to eppendorf tubes and pre-cleared with 10 μlof rabbit pre-immune antibody on a rotator at 4° C. for 1 hr. Forty μlof protein A-Sepharose (Amersham) is then added and incubated at 4° C.overnight on a rotator.

The protein A-Sepharose beads are harvested and the supernatant removedto a fresh eppendorf tube. Immune antibody is added to supernatant androtated for 1 hr at 4° C. Thirty μl of protein A-Sepharose is then addedand the mixture is further rotated at 4° C. for 1 hr. The beads areharvested and the supernatant is aspirated. The beads are washed threetimes with 50 mM Tris (pH 8.0), 150 mM NaCl, 0.1% Triton X-100, 10 mMsodium fluoride, 10 mM sodium pyrophosphate, 10 mM sodium orthovanadate,and 10 mM EDTA. Dry the beads with a 50 μl Hamilton syringe. Laemmliloading buffer containing 100 mM DTT is added to the beads and samplesare boiled for 5 min. The beads are spun down and the supernatant isloaded onto SDS-PAGE gels. Comparison of the control and experimentalsamples allows for the selection of polypeptides that interact with theprotein of interest.

Example 13 Sample for Mass Spectrometry of Interacting Proteins

The gel slices are cut into 1 mm cubes and 10 to 20 μl of 1% acetic acidis added. The gel particles are washed with 100-150 μl of HPLC gradewater (5 minutes with occasional mixing), briefly centrifuged, and theliquid is removed. Acetonitrile (˜200 μl, approximately 3 to 4 times thevolume of the gel particles) is added followed by incubation at roomtemperature for 10 to 15 minutes with vortexing. A second acetonitrilewash may be required to completely dehydrate the gel particles. Thesample is briefly centrifuged and all the liquid is removed.

The protein in the gel particles is reduced at 50 degrees Celsius using10 mM dithiothreitol (in 100 mM ammonium bicarbonate) for 30 minutes andthen alkylated at room temperature in the dark using 55 mM iodoacetamide(in 100 mM ammonium bicarbonate). The gel particles are rinsed with aminimal volume of 100 mM ammonium bicarbonate before a trypsin (50 mMammonium bicarbonate, 5 mM CaCl₂, and 12.5 ng/μl trypsin) solution isadded. The gel particles are left on ice for 30 to 45 minutes (after 20minutes incubation more trypsin solution is added). The excess trypsinsolution is removed and 10 to 15 μl digestion buffer without trypsin isadded to ensure the gel particles remain hydrated during digestion. Thesamples are digested overnight at 37° C.

The following day, the supernatant is removed from the gel particles.The peptides are extracted from the gel particles with 2 changes of 100μL of 100 mM ammonium bicarbonate with shaking for 45 minutes and pooledwith the initial gel supernatant. The extracts are acidified to 1% (v/v)with 100% acetic acid.

(a) Method One for Purification of Tryptic Peptides

The tryptic peptides are purified with a C18 reverse phase resin. 250 μLof dry resin is washed twice with methanol and twice with 75%acetonitrile/1% acetic acid. A 5:1 slurry of solvent:resin is preparedwith 75% acetonitrile/1% acetic acid. To the extracted peptides, 2 μL ofthe resin slurry is added and the solution is shaken at moderate speedfor 30 minutes at room temperature. The supernatant is removed andreplaced with 200 μL of 2% acetonitrile/1% acetic acid and shaken for5-15 minutes with moderate speed. The supernatant is removed and thepeptides are eluted from the resin with 15 μL of 75% acetonitrile/1%acetic acid with shaking for about 5 minutes. The peptide and slurrymixture is applied to a filter plate and centrifuged for 1-2 minutes at1000 rpm, the filtrate is collected and stored at −70° C. until use.

(b) Method Two for Purification of Tryptic Peptides

Alternatively, the tryptic peptides may be purified using ZipTip_(C18)(Millipore, Cat # ZTC18S960). The ZipTips are first pre-wetted byaspirating and dispensing 100% methanol 5 times. The tips are thenwashed with 2% acetonitrile/1% acetic acid (5 times), followed by 65%acetonitrile/1% acetic (5 times) and returned to 2% acetonitrile/1%acetic acid (5 times). The ZipTips are replaced in their rack and theresidual solvent is eliminated. The ZipTips are washed again with 2%acetonitrile/1% acetic acid (5 times). The digested peptides are boundto the ZipTips by aspirating and dispensing the samples 5 times. Saltsare removed by washing ZipTips with 2% acetonitrile/1% acetic acid (5times). 10 μL of 65% acetonitrile/1% acetic acid is collected by theZipTips and dispensed into a 96-well microtitire plate. 1 μL of sampleand 1 μL of matrix are spotted on a MALDI-TOF sample plate for analysis.

Example 14 Mass Spectrometric Analysis of Interacting Proteins

(a) Method One for Analysis of Tryptic Peptides

Analytical samples containing tryptic peptides are subjected to MatrixAssisted Laser Desorption/Ionization Time Of Flight (MALDI-TOF) massspectrometry. Samples are mixed 1:1 with a matrix ofα-cyano-4-hydroxy-trans-cinnamic acid. The sample/matrix mixture isspotted on to the MALDI sample plate with a robot. The sample/matrixmixture is allowed to dry on the plate and is then introduced into themass spectrometer. Analysis of the peptides in the mass spectrometer isconducted using both delayed extraction mode and an ion reflector toensure high resolution of the peptides.

Internally-calibrated tryptic peptide masses are searched against bothin-house proprietary and public databases using a correlative massmatching algorithm. Statistical analysis is performed on each proteinmatch to determine its validity. Typical search constraints includeerror tolerances within 0.1 Da for monoisotopic peptide masses andcarboxyamidomethylation of cysteines. Identified proteins are storedautomatically in a relational database with software links to SDS-PAGEimages and ligand sequences.

(b) Method Two for Analysis of Tryptic Peptides

Alternatively, samples containing tryptic peptides are analyzed with anion trap instrument. The peptide extracts are first dried down toapproximately 1 μL of liquid. To this, 0.1% trifluoroacetic acid (TFA)is added to make a total volume of approximately 5 mL. Approximately 1-2μL of sample are injected onto a capillary column (C8, 150 μm ID, 15 cmlong) and run at a flow rate of 800 nL/min. using the following gradientprogram: Time (minutes) % Solvent A % Solvent B 0 95 5 30 65 35 40 20 8041 95 5

Where Solvent A is composed of water/0.5% acetic acid and Solvent B isacetonitrile/0.5% acetic acid. The majority of the peptides will elutebetween the 20-40% acetonitrile gradient. Two types of data from theeluting HPLC peaks are acquired with the ion trap mass spectrometer. Inthe MS¹ dimension, the mass to charge range for scanning is set at400-1400—this will determine the parent ion spectrum. Secondly, theinstrument has MS² capabilities whereby it will acquire fragmentationspectra of any parent ions whose intensities are detected to be greaterthan a predetermined threshold (Mann and Wilm, Anal Chem 66(24):4390-4399 (1994)). A significant amount of information is collected foreach protein sample as both a parent ion spectrum and many daughter ionspectra are generated with this instrumentation.

All resulting mass spectra are submitted to a database search algorithmfor protein identification. A correlative mass algorithm is utilizedalong with a statistical verification of each match to identify aprotein's identification (Ducret A, et al., Protein Sci 7(3): 706-719(1998)). This method proves much more robust than MALDI-TOF massspectrometry for identifying the components of complex mixtures ofproteins.

Example 15 NMR Analysis

Purified protein sample is centrifuged at 13,000 rpm for 10 minutes witha bench-top microcentrifuge to eliminate any precipitated protein. Thesupernatant is then transferred into a clean tube and the sample volumeis measured. If the sample volume is less than 450 μl, an appropriateamount of crystal buffer is added to the sample to reach that volume.Then 50 μl of D₂O (99.9%) is added to the sample to make an NMR sampleof 500 μl. The usual concentration of the protein sample is usuallyapproximately 1 mmol or greater.

NMR screening experiments are performed on a Bruker AV600 spectrometerequipped with a cryoprobe, or other equivalent instrumentation. Allspectra are recorded at 25° C. Standard 1D proton pulse sequence withpresaturation is used for ID screening. Normally, a sweepwidth of 6400Hz, and eight or sixteen scans are used, although different pulsesequences are known to those of skill in the art and may be readilydetermined. For ¹H, ¹⁵N HSQC experiments, a pulse sequence with“flip-back” water suppression may be used. Typically, sweepwidths of8000 Hz and 2000 Hz are used for F2 and F1 dimension, respectively. Fourto sixteen scans are normally adequate. The data is then processed on aSun Ultra 5 computer with NMR pipe software.

A representative NMR spectrum from a ¹H, ¹⁵N HSQC experiment generatedwith a polypeptide having the amino acid sequence of SEQ ID NO: 4,prepared and purified as described above, is presented in FIG. 8.

Example 16 X-ray Crystallography

(a) Crystallization

The purified protein was stored at 4° C. at a stock concentration of 7.7mg/ml in 0.5 M NaCl/10 mM HEPES buffer pH 7.5, and kept on icethroughout the screening set-ups. Initial screening was completed on thesame day that the protein purification was completed. Aftercentrifugation at 14000 rpm in a microcentrifuge for 10 minutes at 4°C., the protein was screened in the sitting drop format using a 36condition API screen. The protein drops (1.5 μL per well) were placed ina 96 well crystallization plate (manufactured by Douglas Instruments anddistributed by Hampton Research), along with the 36 reservoir solutions(100 μL of each per well). 1.5 μL from each well condition was thenaspirated and dispensed on top of the protein drops. The plates weresealed using clear sealing tape. The completed screen plate was storedin a crystal room maintained at 20° C. and 40% relative humidity. Thescreen was examined under a microscope and crystals were found in thewells after 14 days. Subsequent refinement screens (optimization) fromproteins stored in freezer stock (at −80° C.) lead to diffractionquality crystals in a final buffer consisting of 1.3 M ammonium sulfate,0.2M NaCl and 0.1 M sodium cacodylate pH 6.4. The refinement screenswere set up using the same plate set-up as the initial screen (sittingdrop, in 96 well format, 1.5 μL protein solution+1.5 μL reservoirsolution).

(b) Co-Crystallization

A variety of methods known in the art may be used for preparation ofco-crystals comprising a polypeptide of the invention and one or morecompounds that interact with the subject polypeptides, such as, forexample, an inhibitor, co-factor, substrate, polynucleotide,polypeptide, and/or other molecule. In one exemplary method, crystals ofthe subject polypeptide may be soaked, for an appropriate period oftime, in a solution containing a compound that interacts with a subjectpolypeptide. In another method, solutions of the subject polypeptideand/or compound that interacts with the subject polypeptide may beprepared for crystallization as described above and mixed into theabove-described sitting drops. In certain embodiments, the molecule tobe co-crystallized with the subject polypeptide may be present in thebuffer in the sitting drop prior to addition of the solution comprisingthe subject polypeptide. In other embodiments, the subject polypeptidemay be mixed with another molecule before adding the mixture to thesitting drop. Based on the teachings herein, one of skill in the art maydetermine the co-crystallization method yielding a co-crystal comprisingthe subject polypeptide.

(c) Heavy Atom Substitution

For preparation of crystals containing heavy atoms, crystals of thesubject polypeptide may be soaked in a solution of a compound containingthe appropriate heavy atom for such period as time as may beexperimentally determined is necessary to obtain a useful heavy atomderivative for x-ray purposes. Likewise, for other compounds that may beof interest, including, for example, inhibitors or other molecules thatinteract with the subject polypeptide, crystals of the subjectpolypeptide may be soaked in a solution of such compound for anappropriate period of time.

(d) Data Collection and Processing

Crystals grown in 96 well plates were prepared for freezing by soakingthem for 45 seconds in a solution that consisted of 20% glycerol addedto an 80% volume of the reservoir solution of the drop in which thecrystals were grown. Data were collected from crystals frozen at 100 Kin a cold gas stream generated by an Oxford Cryostream crystal coolingdevice. Data on the E. faecalis selmet protein crystals were collectedat the Advanced Photon Source at Argonne National Labs, COM-CAT beamlineequipped with a MAR CCD detector. Data were indexed, integrated andscaled using DENZO/SCALEPACK (Otwinowski, Z. and Minor, W. (1997)Methods Enzymol. 276:307-326). Strong, coherent scattering by water/icephases compromised data quality and completeness in the 3.7-3.9 Å range.The protein crystallized in space group P4₃2₁2 with unit cell dimensionsa=57.908 Å, b=57.908 Å, c=138.424 Å, a ==γ=90° with one molecule perasymmetric unit.

All phasing calculations, density modification and refinement werecarried out using the CNX suite of programs (Brunger, A. T., et al.(1998) Acta Crystallogr. D. Biol. Crystallogr. 54:905-921). Thestructure was solved by single anomalous diffraction, using phases offthe selenium peak. The quality of the solvent flattened electron densitymaps were good, allowing for a partial automatic build by MAID, followedby manual tracing the polypeptide chain using TURBO-FRODO (Roussel, A.and Cambillau, C. (1989) TURBO-FRODO. Silicon Graphics Geometry PartnerDirectory, Silicon Graphics, Mountain View, Calif.) for interactivemodel building. Ten percent of the reflections were set aside for thecalculation of a free R-factor and the same set of reflections wasmaintained throughout refinement. The structure was refined usingsimulated annealing torsion angle refinement against a maximumlikelihood target that included experimental phase information, usingstandard protocols in CNX. Individual temperature factors were refinedagainst a similar target. Ordered solvent molecules were picked manuallyusing a combination of 2|Fo|-|Fc|αc and |Fo|-|Fc|αc maps in TURBO-FRODO.The sulfate and chloride ions were added in a similar fashion. Rounds ofmodel rebuilding in TURBO alternating with refinement and water pickingwere iterated over multiple cycles until convergence was achieved.Residues 1-3 and residue 189 were not clearly discernable in theelectron density map and were not modeled. Residues 194-201 from theC-terminal histidine tag were found to be structured in the substratebinding pocket, and were modeled in the structure.

Structure solution and refined statistics are reported in Table 3,contained in FIG. 11. FIG. 12 contains a list of the atomic coordinatesof the subject polypeptide and other molecules contained in the crystal.FIG. 13 to FIG. 17 depict various features of the crystal structure andother properties of a subject polypeptide.

(e) Analysis of the X-ray Structure of the Subject Polypeptide

General Description of Structure

The overall fold of the E. faecalis guanylate kinase is similar to theyeast and mouse guanylate kinase structures (FIG. 13). Threestructurally distinct regions, the CORE, LID and NMP-binding regions,can be found in the E. faecalis structure (FIG. 14). The structures ofguanylate kinases have been described as a hand, with the CORE region asthe palm, the LID region as the thumb and the NMP-binding domain as thefingers. These regions have been observed to move with respect to eachother, closing like a fist around the substrates. In E. faecalisguanylate kinase, the CORE region (residues 8-31, 95-122, and 162-189),the LID region (residues 124-154) and NMP-binding domain (residues36-88) are interconnected by four hinges. Such regions, or portionsthereof, may present druggable regions in guanlyate kinase. Theseassignment of these regions is based on the regions defined by ananalysis of the mouse guanylate kinase, wherein the regions are definedon higher RMSD values in the interface between regions of differentguanylate kinases, and not solely on B factor analysis. The NMP-bindingregion and CORE region are connected by two hinges and the CORE and LIDregions are linked with two hinges. The additional C-terminal residuesfound in bacterial, mammalian and plant guanylate kinases, but not theyeast guanylate kinase, are observed as a helix. The function of theseadditional residues remains undetermined. Portions of the C-terminal Histag are also observed in the structure, packed in the binding pocket ofthe neighboring symmetry related molecule.

Active Site and Other Druggable Regions

The potential binding site residues and size and shape of the bindingpocket are shown in FIG. 15 and the table below. Since an overlay of theyeast and E. faecalis structures is difficult (FIG. 16), identificationof the active site residues of E. faecalis guanylate kinase is based onalignment of the mouse and yeast guanylate kinase structures. Theseresidues are fairly well conserved across bacterial species (FIGS. 13,17). Druggable Region Amino Acid Residues Description of Binding SiteDruggable K20 T21 A22 R135 ADP/ATP binding Region I R131 I168 DruggableS35 R40 R43 Y52 E71 GMP binding, arginines may Region II Y80 V82 A99T101 play a role in catalysis R145

The relative orientation of the CORE, LID, and NMP-binding regions arethought to change upon ligand binding, altering the shape and size ofthe binding sites. The binding site for ADP/ATP appears to be locatedbetween the LID and CORE domains. Based on the mouse adenineco-structure, the adenine is believed to be held in position by astrictly conserved Arg/31 via a stacking interaction, and also by themain chain carbonyl of Ile168. The side chain of A sn171 of the mousestructure helps to hold the adenine in position. However, the alignmentof the yeast structure with the mouse structure fails at Asn171. Severalwater molecules in the mouse structure appear to stabilize the ribose ofADP/ATP, and phosphate binding is mediated through the P-loop, which ishighly conserved among ATP-binding proteins. The ADP/ATP binding region,or portions thereof, may present a druggable region in guanylate kinase.The druggable region may comprise at least one of residues Lys20, Thr21,Ala22, Arg135, Arg131, Ile68.

Based on the mouse structure, specificity for GMP in the yeast structureappears to be created by base discrimination interactions. Ser35 mayinteract with the guanine carbonyl at position 6 (an amino group inadenine) while carboxylic acids Glu71 and Thr101 may interact with theguanine amino group at position 3 (not present in adenine). Specificityfor guanine appears further enhanced by Glu71 forming a bidentateinteraction with two hydrogen bond donors: N1, which is protonated inguanine, and the amine at position 2 of the base. The analogous positionin adenylate kinase is filled by Gln, presenting a hydrogen bond donorto the unprotonated N1 and the amine at position 6. The potassiumpresent in the mouse GMP binding site was not observed in the yeaststructure. The GMP binding region, or portions thereof, may present adruggable region in guanylate kinase. The druggable region may compriseat least one of residues Ser35, Arg40, Arg43, Tyr52, Glu71, Tyr80,Val82, Ala99, Tyr101, or Arg145.

Known Inhibitors of Guanylate Kinases

Guanylate kinase catalyzes the rate limiting step in the phosphorylationof thiopurines. Purine base analogs 6-mercaptopurine and 6-thioguaninehave been in clinical use as inhibitors for nearly 50 years. Modeling of6-thioguanosine 5′-monophosphate (6T-MP) in the active site of mouseguanylate kinase showed that the sulfur atom, which substitutes foroxygen in guanine, makes hydrogen bonds with Ser337 and Thr83, possiblycausing steric clashing.

The following table lists known inhibitors and substrates which couldform the basis for design of inhibitors of guanylate kinase, asdetermined from a search of the BRENDA database: Compound SMILES strings(if available) 6-thioguanosine 5′-monophosphateNc1nc2n(cnc2c(═S)[nH]1)[C@@H]3O[C@H](COP(═O)(O)O)[C@@H](O)[C@H]3O8-azaguanosine 5′-diphosphateNc1nc2n(nnc2c(═O)[nH]1)[C@@H]3O[C@H](COP(═O)(O)OP(═O)(O)O)[C@@H](O)[C@H]3O8-azaguanosine 5′-monophosphateNc1nc2n(nnc2c(═O)[nH]1)[C@@H]3O[C@H](COP(═O)(O)O)[C@@H](O)[C@H]3O8-bromoguanosine 5′-diphosphateNc1nc2n([C@@H]3O[C@H](COP(═O)(O)OP(═O)(O)O)[C@@H](O)[C@H]3O)c(Br)nc2c(═O)[nH]18-bromoguanosine 5′-monophosphateNc1nc2n([C@@H]3O[C@H](COP(═O)(O)O)[C@@H](O)[C@H]3O)c(Br)nc2c(═O)[nH]18-thioguanosine 5′-diphosphateNc1nc2n([C@H]3O[C@@H](COP(═O)(O)OP(═O)(O)O)[C@H](O)[C@@H]3O)c(S)nc2c(═O)[nH]19-(1 3-dihydroxy-2- propoxymethyl)guanine 5′-diphosphate 9-(13-dihydroxy-2- propoxymethyl)guanine 5′- monophosphate9-(2-hydroxyethoxymethyl)guanine 5′- diphosphate9-(2-hydroxyethoxymethyl)guanine 5′- monophosphate ADPNc1ncnc2n(cnc12)C3OC(COP(═O)(O)OP(═O)(O)O)C(O)C3O ATPNc1ncnc2n(cnc12)C3OC(COP(═O)(O)OP(═O)(O)OP(═O)(O)O)C(O)C3O dADPNc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](COP(═O)(O)OP(═O)(O)O)O3 dADPNc1ncnc2n(cnc12)C3CC(O)C(COP(═O)(O)OP(═O)(O)OP(═O)(O)O)O3 dGDPNc1nc2n(cnc2c(═O)[nH]1)[C@H]3C[C@H](O)[C@@H](COP(═O)(O)OP(═O)(O)O)O3dGMP Nc1nc2n(cnc2c(═O)[nH]1)[C@H]3C[C@H](O)[C@@H](COP(═O)(O)O)O3 GDPNc1nc2n(cnc2c(═O)[nH]1)[C@@H]3O[C@H](COP(═O)(O)OP(═O)(O)O)[C@@H](O)[C@H]3OGMP Nc1nc2n(cnc2c(═O)[nH]1)[C@@H]3O[C@H](COP(═O)(O)O)[C@@H](O)[C@H]3OIDP OC1C(O)C(OC1COP(═O)(O)OP(═O)(O)O)n2cnc3c(O)ncnc23 IMPO[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(═O)(O)O)n2cnc3c(═O)[nH]cnc23

Comparison to Other Guanylate Kinases

There is low sequence identity between the various nucleosidemonophosphate (NMP) kinases. Since there is structural variation betweenthem, it is difficult to presume the structure of one kinase fromanother. For example, the NMP-binding domain of adenylate kinase is allhelical, whereas the structure of the guanylate kinase has a fourstranded sheet and two short helices. Current medical understanding ofguanylate kinases arises from the apo- and GMP-bound structures of theyeast guanylate kinase and the mouse guanylate kinase (88% identity, 93%homology to human). The structure of the E. faecalis structure is verysimilar to both of these and conforms a conserved structural motif forthe guanylate kinase family. The RMSD between the EF structure and theyeast apo guanylate kinase is 1.68 Å² and the RMSD between the EF andthe yeast GMP complex is 1.72 Å² (FIG. 16).

The induced fit mechanism has been proposed to play an important role incatalysis by guanylate kinases and other NMP kinases. A comparison ofthe structures of nucleotide-free adenylate kinase to both the singlesubstrate-bound kinase and to the double-substrate bound kinase showrigid body movements of three regions, the CORE, LID and NMP-bindingsection, with respect to each other. In the process, the enzyme changesfrom the open apo form to an intermediate where one substrate is boundto a fully closed form in the presence of both substrates. Although therelative conformations of these regions are different between the twoforms in the yeast, mouse, and E. faecalis structures, a comparison ofthe same region in each shows a small RMSD. In the closed conformationof the mouse ternary complex, the ADP is mostly solvent exposed and theGMP is buried. This suggests an ordered substrate binding and releasemechanism; however, kinetic results are consistent with a randomsequential mechanism. The structure may undergo a transient opening andclosing (“breathing”). The structure of one of the more stableconformations has been solved.

Unlike the GMP-binding domain, which moves toward the active center ofthe enzyme upon GMP binding, the LID domain moves away from the activecenter and makes the presumed ATP-binding site more open. Therefore, theLID domain movement may facilitate the binding of Mg.ATP. Severalarginine residues in the LID region of most NMP-kinases, with theexception of eukaryotic thymidylate kinases, have been shown toparticipate in catalysis by direct interaction with the γ-phosphate ofATP. The conformational change seen in the mouse guanylate kinasecostructure positions Arg137 and Arg148 such that they may interact withthe ATP. Mutational studies of analogous arginines in adenylate kinaseshave shown these to be essential for catalysis.

The following table lists the corresponding key residues in the ADP andGMP binding sites in the E. faecalis, mouse, and yeast guanylatekinases, based on the alignment of E. faecalis structures with the mouseand yeast structures. Such residues may comprise a druggable region. E.faecalis Mouse Yeast guanylate guanylate guanylate kinase kinase kinaseADP binding sites K20 K17 K14 T21 S18 S15 A22 T19 T16 R135 R137 R135R131 R133 R131 Not aligned N171 N168 I168 D172 D169 GDP binding site S35S37 S34* R40 R41 R38 R43 R44 R41 Y52 Y53 Y50 E71 E72 E69 Y80 Y81 Y78 V82T83 S80 A99 D101 D98 T101 D103 D100 R145 R148 R144 Not present K+ Notpresent

Based in part on the structural information described above, in oneaspect, the present invention is directed towards druggable regions of asubject polypeptide or other guanylate kinase comprising the majority ofthe amino acid residues contained in a subject druggable region. Inanother aspect, the present invention is directed toward an inhibitorthat interacts with the active or binding site of a guanylate kinase. Inone embodiment, this site is the ADP/ATP binding site. In certainembodiments, the ADP/ATP binding site may be comprised of at least oneof Lys20, Thr21, Ala22, Arg135, Arg131, and Ile168. In anotherembodiment, this site is the GMP binding site. In certain embodiments,the GMP binding site may be comprised of at least one of Ser35, Arg40,Arg43, Tyr52, Glu71, Tyr80, Val82, Ala99, Thr101, and Arg145. In anotheraspect, the present invention is directed towards an inhibitor thatinteracts with the hinge regions of a guanylate kinase so as to precludeit from moving, thereby inhibiting such enzyme.

Example 17 Annotations

The functional annotation is arrived at by comparing the amino acidsequence of the ORF against all available ORFs in the NCBI databaseusing BLAST. The closest match is selected to provide the probablefunction of the polypeptide having the sequence of SEQ ID NO: 2. Resultsof this comparison are described above and set forth in Table 2 of FIG.7.

The COGs database (Tatusov R L, Koonin E V, Lipman D J. Science 1997;278 (5338) 631-37) classifies proteins encoded in twenty-one completedgenomes on the basis of sequence similarity. Members of the same Clusterof Orthologous Group, (“COG”), are expected to have the same or similardomain architecture and the same or substantially similar biologicalactivity. The database may be used to predict the function ofuncharacterised proteins through their homology to characterizedproteins. The COGs database may be searched from NCBI's website(http://www.ncbi.nlm.nih.gov/COG/) to determine functional annotationdescriptions, such as “information storage and processing” (translation,ribosomal structure and biogenesis, transcription, DNA replication,recombination and repair); “cellular processes” (cell division andchromosome partitioning, post-translational modification, proteinturnover, chaperones, cell envelope biogenesis, outer membrane, cellmotility and secretion, inorganic ion transport and metabolism, signaltransduction mechanisms); or “metabolism” (energy production andconversion, carbohydrate transport and metabolism, amino acid transportand metabolism, nucleotide transport and metabolism, coenzymemetabolism, lipid metabolism). For certain polypeptides, there is noentry available. Results of this analysis are described above and setforth in Table 2 of FIG. 7.

Example 18 Essential Gene Analysis

SEQ ID NO: 2 is compared to a number of publicly available “essentialgenes” lists to determine whether that protein is encoded by anessential gene. An example of such a list is descended from a freerelease at the www.shigen.nig.ac.ip PEC (profiling of E. colichromosome) site, http://www.shigen.nip.ac.jp/ecoli/pec/. The list isprepared as follows: a wildcard search for all genes in class“essential” yields the list of essential E. coli proteins encoded byessential genes, which number 230. These 230 hits are pruned bycomparing against an NCBI E. coli genome. Only 216 of the 230 genes onthe list are found in the NCBI genome. These 216 are termed theessential-216-ecoli list. The essential-216-ecoli list is used to garner“essential” genes lists for other microbial genomes by blasting. Forinstance, formatting the 216-ecoli as a BLAST database, then BLASTing agenome (e.g. S. aureus) against it, elucidates all S. aureus genes withsignificant homology to a gene in the 216-essential list. SEQ ID NO: 2is compared against the appropriate list and a match with a score ofe⁻²⁵ or better is considered an essential gene according to that list.In addition to the list described above, other lists of essential genesare publicly available or may be determined by methods disclosedpublicly, and such lists and methods are considered in deciding whethera gene is essential. See, for example, Thanassi et al., Nucleic AcidsRes 2002 Jul. 15; 30(14):3152-62; Forsyth et al., Mol Microbiol 2002March; 43(6):1387-400; Ji et al., Science 2001 Sep. 21;293(5538):2266-9; Sassetti et al., Proc Natl Acad Sci USA 2001 Oct. 23;98(22):12712-7; Reich et al., J Bacteriol 1999 August; 181(16):4961-8;Akerley et al., Proc Natl Acad Sci USA 2002 Jan. 22; 99(2):966-71).Also, other methods are known in the art for determing whether a gene isessential, such as that disclosed in U.S. patent application Ser. No.10/202,442 (filed Jul. 24, 2002). The conclusion as to whether the geneencoding the amino acid sequence set forth in SEQ ID NO: 2 is essentialis set forth in Table 2 of FIG. 7.

Example 19 PDB Analysis

SEQ ID NO: 2 is compared against the amino acid sequences in a databaseof proteins whose structures have been solved and released to the PDB(protein data bank). The identity/information about the top PDB homolog(most similar “hit”, if any; a PDB entry is only considered a hit if thescore is e⁻⁴ or better) is annotated, and the percent similarity andidentity between SEQ ID NO: 2 and the closest hit is calculated, withboth being indicated in Table 2 of FIG. 7.

Example 20 Virtual Genome Analysis

VGDB or VG is a queryable collection of microbial genome databasesannotated with biophysical and protein information. The organismspresent in VG include: Genome file File GRAM Species Source dateecoli.faa G− Escherichia coli NCBI Nov. 18, 1998 hpyl.faa G−Helicobacter pylori NCBI Apr. 19, 1999 paer.faa G− Pseudomonas NCBI Sep.22, 2000 aeruginosa ctra.faa G− Chlamydia trachomatis NCBI Dec. 22, 1999hinf.faa G− Haemophilus influenzae NCBI Nov. 26, 1999 nmen.faa G−Neisseria meningitidis NCBI Dec. 28, 2000 rpxx.faa G− Rickettsiaprowazekii NCBI Dec. 22, 1999 bbur.faa G− Borrelia burgdorferi NCBI Nov.11, 1998 bsub.faa G+ Bacillus subtilis NCBI Dec. 1, 1999 staph.faa G+Staphylococcus aureus TIGR Mar. 8, 2001 spne.faa G+ Streptococcus TIGRFeb. 22, 2001 pneumoniae mgen.faa G+ Mycoplasma genitalium NCBI Nov. 23,1999 efae.faa G+ Enterococcus faecalis TIGR Mar. 8, 2001

The VGDB comprises 13 microbial genomes, annotated with biophysicalinformation (pI, MW, etc), and a wealth of other information. These 13organism genomes are stored in a single flatfile (the VGDB) againstwhich PSI-blast queries can be done.

SEQ ID NO: 2 is queried against the VGDB to determine whether thissequence is found, conserved, in many microbial genomes. There arecertain criteria that must be met for a positive hit to be returned(beyond the criteria inherent in a basic PSI-blast).

When an ORF is queried it may have a maximum of 13 VG-organism hits. Ahit is classified as such as long as it matches the following criteria:Minimum Length (as percentage of query length): 75 (Ensure hit proteinis at least 75% as long as query); Maximum Length (as percentage ofquery length): 125 (Ensure hit protein is no more than 125% as long asquery); eVal:-10 (Ensure hit has an e-Value of e-10 or better); Id%:>:25 (Ensure hit protein has at least 25% identity to query). Thee-Value is a standard parameter of BLAST sequence comparisons, andrepresents a measure of the similarity between two sequences based onthe likelihood that any similarities between the two sequences couldhave occurred by random chance alone. The lower the e-Value, the lesslikely that the similarities could have occurred randomly and,generally, the more similar the two sequences are.

The organisms having an orthologue of the polypeptide having SEQ ID NO:2 are listed in Table 2, shown in FIG. 7.

Example 21 Epitopic Regions

The three most likely epitopic regions of a polypeptide having SEQ IDNO: 2 are predicted using the semi-empirical method of Kolaskar andTongaonkar (FEBS Letters 1990 v276 172-174), the software package calledProtean (DNASTAR), or MacVectors's Protein analysis tools (Accerlyrs).The antigenic propensity of each amino acid is calculated by the ratiobetween frequency of occurrence of amino acids in 169 antigenicdeterminants experimentally determined and the calculated frequency ofoccurrence of amino acids at the surface of protein. The results ofthese bioinformatics analyses are presented in Table 2, shown in FIG. 7.

EQUIVALENTS

The present invention provides among other things, novel proteins,protein structures and protein-protein interactions. While specificembodiments of the subject invention have been discussed, the abovespecification is illustrative and not restrictive. Many variations ofthe invention will become apparent to those skilled in the art uponreview of this specification. The full scope of the invention should bedetermined by reference to the claims, along with their full scope ofequivalents, and the specification, along with such variations.

All publications and patents mentioned herein, including those itemslisted below, are hereby incorporated by reference in their entirety asif each individual publication or patent was specifically andindividually indicated to be incorporated by reference. In case ofconflict, the present application, including any definitions herein,will control. To the extent that any U.S. Provisional PatentApplications to which this patent application claims priorityincorporate by reference another U.S. Provisional Patent Application,such other U.S. Provisional Patent Application is not incorporated byreference herein unless this patent application expressly incorporatesby reference, or claims priorty to, such other U.S. Provisional PatentApplication.

Also incorporated by reference in their entirety are any polynucleotideand polypeptide sequences which reference an accession numbercorrelating to an entry in a public database, such as those maintainedby The Institute for Genomic Research (TIGR) (www.tigr.org) and/or theNational Center for Biotechnology Information (NCBI)(www.ncbi.nlm.nih.gov).

Also incorporated by reference are the following: WO 00/45168, WO00/79238, WO 00/77712, EP 1047108, EP 1047107, WO 00/72004, WO 00/73787,WO00/67017, WO 00/48004, WO 01/48209, WO 00/45168, WO 00/45164, U.S.Ser. No. 09/720,272; PCT/CA99/00640; U.S. patent application Ser. No.10/097,125 (filed Mar. 12, 2002); Ser. No. 10/097,193 (filed Mar. 12,2002); Ser. No. 10/202,442 (filed Jul. 24, 2002); Ser. No. 10/097,194(filed Mar. 12, 2002); Ser. No. 09/671,817 (filed Sep. 17, 2000); Ser.No. 09/965,654 (filed Sep. 27, 2001); Ser. No. 09/727,812 (filed Nov.30, 2000); 60/370,667 (filed Apr. 8, 2002); a utility patent applicationentited “Methods and Appartuses for Purification” (filed Sep. 18, 2002);U.S. Pat. Nos. 6,451,591; 6,254,833; 6,232,114; 6,229,603; 6,221,612;6,214,563; 6,200,762; 6,171,780; 6,143,492; 6,124,128; 6,107,477;D428157; 6,063,338; 6,004,808; 5,985,214; 5,981,200; 5,928,888;5,910,287; 6,248,550; 6,232,114; 6,229,603; 6,221,612; 6,214,563;6,200,762; 6,197,928; 6,180,411; 6,171,780; 6,150,176; 6,140,132;6,124,128; 6,107,066; 6,270,988; 6,077,707; 6,066,476; 6,063,338;6,054,321; 6,054,271; 6,046,925; 6,031,094; 6,008,378; 5,998,204;5,981,200; 5,955,604; 5,955,453; 5,948,906; 5,932,474; 5,925,558;5,912,137; 5,910,287; 5,866,548; 6,214,602; 5,834,436; 5,777,079;5,741,657; 5,693,521; 5,661,035; 5,625,048; 5,602,258; 5,552,555;5,439,797; 5,374,710; 5,296,703; 5,283,433; 5,141,627; 5,134,232;5,049,673; 4,806,604; 4,689,432; 4,603,209; 6,217,873; 6,174,530;6,168,784; 6,271,037; 6,228,654; 6,184,344; 6,040,133; 5,910,437;5,891,993; 5,854,389; 5,792,664; 6,248,558; 6,341,256; 5,854,922; and5,866,343.

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1. A composition comprising an isolated, recombinant polypeptide,wherein the polypeptide comprises: (a) an amino acid sequence set forthin SEQ ID NO: 2 or SEQ ID NO: 4; (b) an amino acid sequence having atleast about 95% identity with the amino acid sequence set forth in SEQID NO: 2 or SEQ ID NO: 4; or (c) an amino acid sequence encoded by apolynucleotide that hybridizes under stringent conditions to thecomplementary strand of a polynucleotide having SEQ ID NO: 1 or SEQ IDNO: 3 and has at least one biological activity of guanylate kinase fromE. faecalis; and wherein the polypeptide of (a), (b) or (c) is at leastabout 90% pure in a sample of the composition.
 2. The composition ofclaim 1, wherein the polypeptide is at least about 95% pure asdetermined by gel electrophoresis.
 3. The composition of claim 1,wherein at least about two-thirds of the polypeptide in the sample issoluble.
 4. The composition of claim 1, wherein the polypeptide is fusedto at least one heterologous polypeptide that increases the solubilityor stability of the polypeptide.
 5. The composition of claim 1, whereinthe composition is crystallized.
 6. The crystallized composition ofclaim 5 further comprising a co-factor.
 7. The crystallized compositionof claim 5, further comprising a small molecule.
 8. The crystallizedcomposition of claim 5, which diffracts x-rays to a resolution of about3.5 Å or better.
 9. The crystallized composition of claim 5, wherein thecrystallized composition has a P4₃2₁2 space group.
 10. A method forobtaining structural information of a crystallized polypeptide, themethod comprising preparing a crystallized composition of claim 5capable of diffracting X-rays to a resolution of 3.5 Å or better; andanalyzing the crystallized polypeptide by X-ray diffraction to determinethe three-dimensional structure of at least a portion of thecrystallized polypeptide comprising said composition.
 11. The method ofclaim 10, wherein the crystallized composition further comprises a smallorganic molecule.
 12. A method for identifying a druggable region of apolypeptide, the method comprising: (a) obtaining a crystallizedcomposition of claim 5, such that the three dimensional structure of thesecond crystallized polypeptide may be determined to a resolution of 3.5Å or better; (b) determining the three dimensional structure of thepolypeptide using X-ray diffraction; and (c) identifying a druggableregion of the polypeptide based on the three-dimensional structure ofthe polypeptide.
 13. A method for identifying a modulator of apolypeptide, the method comprising: (a) providing the three-dimensionalcoordinates for a plurality of the amino acids of a polypeptidecomprising (1) an amino acid sequence set forth in SEQ ID NO: 2 or SEQID NO: 4; (2) an amino acid sequence having at least about 95% identitywith the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4;or (3) an amino acid sequence encoded by a polynucleotide thathybridizes under stringent conditions to the complementary strand of apolynucleotide having SEQ ID NO: 1 or SEQ ID NO: 3 and has at least onebiological activity of guanylate kinase from E. faecalis; such thatcrystals of the crystallized polypeptide will diffract x-rays to aresolution of 5 Å or better; (b) identifying a druggable region of thepolypeptide; and (c) selecting at least one potential modulator by usingthe three dimensional coordinates to determine if a chemical entity maybind to or interfere with the druggable region.
 14. The method of claim13, wherein the chemical entity is a small molecule.
 15. The method ofclaim 13, wherein the chemical entity is selected from a database orlibrary of chemical entities.
 16. The method of claim 13, furthercomprising: (d) contacting a polypeptide comprising: (1) an amino acidsequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (2) an amino acidsequence having at least about 95% identity with the amino acid sequenceset forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (3) an amino acid sequenceencoded by a polynucleotide that hybridizes under stringent conditionsto the complementary strand of a polynucleotide having SEQ ID NO: 1 orSEQ ID NO: 3 and has at least one biological activity of guanylatekinase from E. faecalis; and (e) assaying the activity of thepolypeptide after contact with the potential modulator, wherein a changein the activity of the polypeptide indicates that the potentialmodulator is a modulator of said polypeptide.
 17. A method for designinga modulator for the prevention or treatment of a E. faecalis relateddisease or disorder, comprising: (a) providing the three dimensionalstructure of a crystallized polypeptide comprising: i) an amino acidsequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (ii) an amino acidsequence having at least about 95% identity with the amino acid sequenceset forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (iii) an amino acidsequence encoded by a polynucleotide that hybridizes under stringentconditions to the complementary strand of a polynucleotide having SEQ IDNO: 1 or SEQ ID NO: 3 and has at least one biological activity ofguanylate kinase from E. faecalis; and (b) designing a potentialmodulator for the prevention or treatment of a a E. faecalis relateddisease or disorder by employing the three-dimensional structure in arational drug design method.
 18. The method of claim 17, furthercomprising (c) contacting E. faecalis or a polypeptide comprising i) anamino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; (ii) anamino acid sequence having at least about 95% identity with the aminoacid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 4; or (iii) anamino acid sequence encoded by a polynucleotide that hybridizes understringent conditions to the complementary strand of a polynucleotidehaving SEQ ID NO: 1 or SEQ ID NO: 3 and has at least one biologicalactivity of guanylate kinase from E. faecalis with the potentialmodulator; and (d) assaying the activity of the polypeptide ordetermining the viability of E. faecalis after contact with themodulator, wherein a change in the activity of the polypeptide or theviability of E. faecalis indicates that the modulator may be useful forprevention or treatment of a E. faecalis related disease or disorder.19. The method of claim 17, wherein said rational drug design methodcomprises performing a fitting operation between the structure of achemical entity and a druggable region of the polypeptide, followed bycomputationally analyzing the results of the fitting operation toquantify the association between the chemical entity and the druggableregion.
 20. The method of claim 17, wherein said rational drug designmethod comprises determining whether a chemical entity is expected tobind to or interfere with the polypeptide.